9IGT | pdb_00009igt

Assembly intermediate of human mitochondrial ribosome small subunit bound to METTL15, RBFA, and mtIF2 (State M2.1)

PDB DOI: https://doi.org/10.2210/pdb9IGT/pdb
EM Map EMD-52857: EMDB EMDataResource
NAKB: 9IGT

Classification: RIBOSOME
Organism(s): Homo sapiens
Mutation(s): Yes

Deposited: 2025-02-20 Released: 2026-03-11
Deposition Author(s): Khawaja, A., Singh, V., Shiriaev, D.I., Rorbach, J.
Funding Organization(s): Knut and Alice Wallenberg Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 5.96 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural analysis reveals alternative pathways for assembly of the human mitoribosome small subunit

Singh, V., Shiriaev, D.I., Bilalli, L., Khawaja, A., Rorbach, J.

To be published.

Macromolecule Content

Total Structure Weight: 1,296.1 kDa
Atom Count: 71,726
Modeled Residue Count: 7,292
Deposited Residue Count: 9,610
Unique protein chains: 33
Unique nucleic acid chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S2, mitochondrial	A [auth B]	296	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y399 (Homo sapiens) Explore Q9Y399 Go to UniProtKB: Q9Y399
PHAROS: Q9Y399 GTEx: ENSG00000122140
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y399
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S24, mitochondrial	B [auth C]	167	Homo sapiens	Mutation(s): 0
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Find proteins for Q96EL2 (Homo sapiens) Explore Q96EL2 Go to UniProtKB: Q96EL2
GTEx: ENSG00000062582
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q96EL2
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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S5, mitochondrial	C [auth D]	430	Homo sapiens	Mutation(s): 0
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Find proteins for P82675 (Homo sapiens) Explore P82675 Go to UniProtKB: P82675
PHAROS: P82675 GTEx: ENSG00000144029
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82675
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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S6, mitochondrial	D [auth E]	125	Homo sapiens	Mutation(s): 0
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Find proteins for P82932 (Homo sapiens) Explore P82932 Go to UniProtKB: P82932
PHAROS: P82932 GTEx: ENSG00000243927
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82932
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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S7, mitochondrial	E [auth F]	242	Homo sapiens	Mutation(s): 0
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Find proteins for Q9Y2R9 (Homo sapiens) Explore Q9Y2R9 Go to UniProtKB: Q9Y2R9
PHAROS: Q9Y2R9 GTEx: ENSG00000125445
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y2R9
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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S9, mitochondrial	F [auth G]	396	Homo sapiens	Mutation(s): 0
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Find proteins for P82933 (Homo sapiens) Explore P82933 Go to UniProtKB: P82933
PHAROS: P82933 GTEx: ENSG00000135972
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UniProt Group	P82933
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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S10, mitochondrial	G [auth H]	201	Homo sapiens	Mutation(s): 0
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Find proteins for P82664 (Homo sapiens) Explore P82664 Go to UniProtKB: P82664
PHAROS: P82664 GTEx: ENSG00000048544
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82664
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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S11, mitochondrial	H [auth I]	194	Homo sapiens	Mutation(s): 1
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Find proteins for P82912 (Homo sapiens) Explore P82912 Go to UniProtKB: P82912
PHAROS: P82912 GTEx: ENSG00000181991
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82912
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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S12, mitochondrial	I [auth J]	138	Homo sapiens	Mutation(s): 0
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Find proteins for O15235 (Homo sapiens) Explore O15235 Go to UniProtKB: O15235
PHAROS: O15235 GTEx: ENSG00000128626
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UniProt Group	O15235
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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S14, mitochondrial	J [auth K]	128	Homo sapiens	Mutation(s): 0
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Find proteins for O60783 (Homo sapiens) Explore O60783 Go to UniProtKB: O60783
PHAROS: O60783 GTEx: ENSG00000120333
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UniProt Group	O60783
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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S15, mitochondrial	K [auth L]	257	Homo sapiens	Mutation(s): 0
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Find proteins for P82914 (Homo sapiens) Explore P82914 Go to UniProtKB: P82914
PHAROS: P82914 GTEx: ENSG00000116898
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P82914
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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S16, mitochondrial	L [auth M]	137	Homo sapiens	Mutation(s): 0
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Find proteins for Q9Y3D3 (Homo sapiens) Explore Q9Y3D3 Go to UniProtKB: Q9Y3D3
PHAROS: Q9Y3D3 GTEx: ENSG00000182180
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UniProt Group	Q9Y3D3
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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S17, mitochondrial	M [auth N]	130	Homo sapiens	Mutation(s): 0
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Find proteins for Q9Y2R5 (Homo sapiens) Explore Q9Y2R5 Go to UniProtKB: Q9Y2R5
PHAROS: Q9Y2R5 GTEx: ENSG00000239789
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UniProt Group	Q9Y2R5
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Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S18b, mitochondrial	N [auth O]	258	Homo sapiens	Mutation(s): 0
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Find proteins for Q9Y676 (Homo sapiens) Explore Q9Y676 Go to UniProtKB: Q9Y676
PHAROS: Q9Y676 GTEx: ENSG00000204568
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9Y676
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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S18c, mitochondrial	O [auth P]	142	Homo sapiens	Mutation(s): 0
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Find proteins for Q9Y3D5 (Homo sapiens) Explore Q9Y3D5 Go to UniProtKB: Q9Y3D5
PHAROS: Q9Y3D5 GTEx: ENSG00000163319
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UniProt Group	Q9Y3D5
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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
MRPS21 isoform 1	P [auth Q]	87	Homo sapiens	Mutation(s): 1
UniProt
Find proteins for A0A2J8VEN6 (Pongo abelii) Explore A0A2J8VEN6 Go to UniProtKB: A0A2J8VEN6
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UniProt Group	A0A2J8VEN6
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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S22, mitochondrial	Q [auth R]	360	Homo sapiens	Mutation(s): 0
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Find proteins for P82650 (Homo sapiens) Explore P82650 Go to UniProtKB: P82650
PHAROS: P82650 GTEx: ENSG00000175110
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UniProt Group	P82650
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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S23, mitochondrial	R [auth S]	190	Homo sapiens	Mutation(s): 0
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Find proteins for Q9Y3D9 (Homo sapiens) Explore Q9Y3D9 Go to UniProtKB: Q9Y3D9
PHAROS: Q9Y3D9 GTEx: ENSG00000181610
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UniProt Group	Q9Y3D9
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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S25, mitochondrial	S [auth T]	173	Homo sapiens	Mutation(s): 0
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Find proteins for P82663 (Homo sapiens) Explore P82663 Go to UniProtKB: P82663
PHAROS: P82663 GTEx: ENSG00000131368
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UniProt Group	P82663
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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S26, mitochondrial	T [auth U]	205	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BYN8 (Homo sapiens) Explore Q9BYN8 Go to UniProtKB: Q9BYN8
GTEx: ENSG00000125901
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UniProt Group	Q9BYN8
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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S27, mitochondrial	U [auth V]	414	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92552 (Homo sapiens) Explore Q92552 Go to UniProtKB: Q92552
PHAROS: Q92552 GTEx: ENSG00000113048
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UniProt Group	Q92552
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S28, mitochondrial	V [auth W]	187	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Q9 (Homo sapiens) Explore Q9Y2Q9 Go to UniProtKB: Q9Y2Q9
PHAROS: Q9Y2Q9 GTEx: ENSG00000147586
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UniProt Group	Q9Y2Q9
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S29, mitochondrial	W [auth X]	398	Homo sapiens	Mutation(s): 0 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P51398 (Homo sapiens) Explore P51398 Go to UniProtKB: P51398
PHAROS: P51398 GTEx: ENSG00000132676
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UniProt Group	P51398
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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S31, mitochondrial	X [auth Y]	395	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q92665 (Homo sapiens) Explore Q92665 Go to UniProtKB: Q92665
PHAROS: Q92665 GTEx: ENSG00000102738
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UniProt Group	Q92665
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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S33, mitochondrial	Y [auth Z]	106	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y291 (Homo sapiens) Explore Q9Y291 Go to UniProtKB: Q9Y291
PHAROS: Q9Y291 GTEx: ENSG00000090263
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UniProt Group	Q9Y291
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S34, mitochondrial	Z [auth 0]	218	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P82930 (Homo sapiens) Explore P82930 Go to UniProtKB: P82930
PHAROS: P82930 GTEx: ENSG00000074071
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UniProt Group	P82930
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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
28S ribosomal protein S35, mitochondrial	AA [auth 1]	323	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P82673 (Homo sapiens) Explore P82673 Go to UniProtKB: P82673
PHAROS: P82673 GTEx: ENSG00000061794
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UniProt Group	P82673
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Aurora kinase A-interacting protein	BA [auth 3]	199	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NWT8 (Homo sapiens) Explore Q9NWT8 Go to UniProtKB: Q9NWT8
PHAROS: Q9NWT8 GTEx: ENSG00000175756
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UniProt Group	Q9NWT8
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Pentatricopeptide repeat domain-containing protein 3, mitochondrial	CA [auth 4]	689	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EY7 (Homo sapiens) Explore Q96EY7 Go to UniProtKB: Q96EY7
PHAROS: Q96EY7 GTEx: ENSG00000132300
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UniProt Group	Q96EY7
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
12S rRNA N4-methylcytidine (m4C) methyltransferase	DA [auth b]	407	Homo sapiens	Mutation(s): 0 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for A6NJ78 (Homo sapiens) Explore A6NJ78 Go to UniProtKB: A6NJ78
PHAROS: A6NJ78 GTEx: ENSG00000169519
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UniProt Group	A6NJ78
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Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
Translation initiation factor IF-2, mitochondrial	FA [auth 7]	691	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P46199 (Homo sapiens) Explore P46199 Go to UniProtKB: P46199
PHAROS: P46199 GTEx: ENSG00000085760
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P46199
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Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
Large ribosomal subunit protein bL12m, short mature form	GA [auth t]	71	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P52815 (Homo sapiens) Explore P52815 Go to UniProtKB: P52815
PHAROS: P52815 GTEx: ENSG00000262814
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UniProt Group	P52815
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Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative ribosome-binding factor A, mitochondrial	HA [auth a]	302	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N0V3 (Homo sapiens) Explore Q8N0V3 Go to UniProtKB: Q8N0V3
PHAROS: Q8N0V3 GTEx: ENSG00000101546
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UniProt Group	Q8N0V3
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Molecule	Chains	Length	Organism
Entity ID: 31
12S mitochondrial rRNA	EA [auth A]	954	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAD Query on NAD Download:Ideal Coordinates CCD File SDF format, chain OA [auth A] MOL2 format, chain OA [auth A] mmCIF format, chain OA [auth A]	OA [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain OA [auth A] Interactions & Density Focus chain OA [auth A]
ATP Query on ATP Download:Ideal Coordinates CCD File SDF format, chain MA [auth X] MOL2 format, chain MA [auth X] mmCIF format, chain MA [auth X]	MA [auth X]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain MA [auth X] Interactions & Density Focus chain MA [auth X]
GDP Query on GDP Download:Ideal Coordinates CCD File SDF format, chain BB [auth 7] SDF format, chain NA [auth X] MOL2 format, chain BB [auth 7] MOL2 format, chain NA [auth X] mmCIF format, chain BB [auth 7] mmCIF format, chain NA [auth X]	BB [auth 7], NA [auth X]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain BB [auth 7] Focus chain NA [auth X] Interactions & Density Focus chain BB [auth 7] Focus chain NA [auth X]
SPM Query on SPM Download:Ideal Coordinates CCD File SDF format, chain PA [auth A] MOL2 format, chain PA [auth A] mmCIF format, chain PA [auth A]	PA [auth A]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain PA [auth A] Interactions & Density Focus chain PA [auth A]
FES Query on FES Download:Ideal Coordinates CCD File SDF format, chain KA [auth P] SDF format, chain LA [auth T] MOL2 format, chain KA [auth P] MOL2 format, chain LA [auth T] mmCIF format, chain KA [auth P] mmCIF format, chain LA [auth T]	KA [auth P], LA [auth T]	FE2/S2 (INORGANIC) CLUSTER Fe₂ S₂ NIXDOXVAJZFRNF-UHFFFAOYSA-N		Interactions Focus chain KA [auth P] Focus chain LA [auth T] Interactions & Density Focus chain KA [auth P] Focus chain LA [auth T]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain JA [auth O] MOL2 format, chain JA [auth O] mmCIF format, chain JA [auth O]	JA [auth O]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain JA [auth O] Interactions & Density Focus chain JA [auth O]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AB [auth A] SDF format, chain QA [auth A] SDF format, chain SA [auth A] SDF format, chain UA [auth A] SDF format, chain WA [auth A] SDF format, chain XA [auth A] SDF format, chain YA [auth A] SDF format, chain ZA [auth A] SDF format, chain VA [auth A] SDF format, chain TA [auth A] SDF format, chain RA [auth A] SDF format, chain IA [auth B] MOL2 format, chain AB [auth A] MOL2 format, chain QA [auth A] MOL2 format, chain SA [auth A] MOL2 format, chain UA [auth A] MOL2 format, chain WA [auth A] MOL2 format, chain XA [auth A] MOL2 format, chain YA [auth A] MOL2 format, chain ZA [auth A] MOL2 format, chain VA [auth A] MOL2 format, chain TA [auth A] MOL2 format, chain RA [auth A] MOL2 format, chain IA [auth B] mmCIF format, chain AB [auth A] mmCIF format, chain QA [auth A] mmCIF format, chain SA [auth A] mmCIF format, chain UA [auth A] mmCIF format, chain WA [auth A] mmCIF format, chain XA [auth A] mmCIF format, chain YA [auth A] mmCIF format, chain ZA [auth A] mmCIF format, chain VA [auth A] mmCIF format, chain TA [auth A] mmCIF format, chain RA [auth A] mmCIF format, chain IA [auth B]	AB [auth A] IA [auth B] QA [auth A] RA [auth A] SA [auth A] AB [auth A], IA [auth B], QA [auth A], RA [auth A], SA [auth A], TA [auth A], UA [auth A], VA [auth A], WA [auth A], XA [auth A], YA [auth A], ZA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AB [auth A] Focus chain IA [auth B] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A] Interactions & Density Focus chain AB [auth A] Focus chain IA [auth B] Focus chain QA [auth A] Focus chain RA [auth A] Focus chain SA [auth A] Focus chain TA [auth A] Focus chain UA [auth A] Focus chain VA [auth A] Focus chain WA [auth A] Focus chain XA [auth A] Focus chain YA [auth A] Focus chain ZA [auth A]