9HBA | pdb_00009hba

Crystal structure of C35 bound to Hem

PDB DOI: https://doi.org/10.2210/pdb9HBA/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2024-11-05 Released: 2025-11-19
Deposition Author(s): Brear, P., Marchesani, F., De Bei, O., Spyrakis, F., Lazzarato, L., Ronda, L.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.51 Å
R-Value Free:
0.215 (Depositor), 0.224 (DCC)
R-Value Work:
0.184 (Depositor), 0.195 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of C35 bound to Hem

Marchesani, F., De Bei, O., Brear, P., Spyrakis, F., Lazzarato, L., Ronda, L.

To be published.

Macromolecule Content

Total Structure Weight: 68.83 kDa
Atom Count: 5,136
Modeled Residue Count: 572
Deposited Residue Count: 574
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A, C	141	Homo sapiens	Mutation(s): 0 Gene Names: HBA1, HBA2
UniProt & NIH Common Fund Data Resources
Find proteins for P69905 (Homo sapiens) Explore P69905 Go to UniProtKB: P69905
PHAROS: P69905 GTEx: ENSG00000188536 ENSG00000206172
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69905
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B, D	146	Homo sapiens	Mutation(s): 0 Gene Names: HBB
UniProt & NIH Common Fund Data Resources
Find proteins for P68871 (Homo sapiens) Explore P68871 Go to UniProtKB: P68871
PHAROS: P68871 GTEx: ENSG00000244734
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P68871
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain JA [auth C] SDF format, chain S [auth B] SDF format, chain QA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain S [auth B] MOL2 format, chain QA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain S [auth B] mmCIF format, chain QA [auth D]	E [auth A], JA [auth C], QA [auth D], S [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain JA [auth C] Focus chain QA [auth D] Focus chain S [auth B]
A1ITR (Subject of Investigation/LOI) Query on A1ITR Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain HA [auth C] SDF format, chain U [auth B] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth C] MOL2 format, chain U [auth B] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth C] mmCIF format, chain U [auth B]	G [auth A], HA [auth C], U [auth B]	4-[2-[[5-(1H-indol-3-yl)-1,3,4-oxadiazol-2-yl]sulfanyl]ethanoylamino]benzoic acid C₁₉ H₁₄ N₄ O₄ S DHEYLYPADJBRNO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain HA [auth C] Focus chain U [auth B] Interactions & Density Focus chain G [auth A] Focus chain HA [auth C] Focus chain U [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain GA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain PA [auth C] SDF format, chain Q [auth A] SDF format, chain TA [auth D] SDF format, chain UA [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain TA [auth D] MOL2 format, chain UA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain TA [auth D] mmCIF format, chain UA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], GA [auth B], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], Q [auth A], TA [auth D], UA [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain TA [auth D] Focus chain UA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain GA [auth B] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain Q [auth A] Focus chain TA [auth D] Focus chain UA [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain IA [auth C] SDF format, chain K [auth A] SDF format, chain MA [auth C] SDF format, chain VA [auth D] SDF format, chain Y [auth B] MOL2 format, chain F [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain VA [auth D] MOL2 format, chain Y [auth B] mmCIF format, chain F [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain VA [auth D] mmCIF format, chain Y [auth B]	F [auth A] IA [auth C] K [auth A] MA [auth C] VA [auth D] F [auth A], IA [auth C], K [auth A], MA [auth C], VA [auth D], Y [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain IA [auth C] Focus chain K [auth A] Focus chain MA [auth C] Focus chain VA [auth D] Focus chain Y [auth B] Interactions & Density Focus chain F [auth A] Focus chain IA [auth C] Focus chain K [auth A] Focus chain MA [auth C] Focus chain VA [auth D] Focus chain Y [auth B]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain SA [auth D] SDF format, chain T [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth B] SDF format, chain R [auth B] SDF format, chain M [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain R [auth B] MOL2 format, chain M [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain R [auth B] mmCIF format, chain M [auth A]	H [auth A] I [auth A] M [auth A] R [auth B] SA [auth D] H [auth A], I [auth A], M [auth A], R [auth B], SA [auth D], T [auth B], V [auth B], Z [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain V [auth B] Focus chain Z [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain SA [auth D] Focus chain T [auth B] Focus chain V [auth B] Focus chain Z [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C]	L [auth A], LA [auth C]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain LA [auth C] Interactions & Density Focus chain L [auth A] Focus chain LA [auth C]
CMO Query on CMO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain KA [auth C] SDF format, chain W [auth B] SDF format, chain RA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain W [auth B] MOL2 format, chain RA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain W [auth B] mmCIF format, chain RA [auth D]	J [auth A], KA [auth C], RA [auth D], W [auth B]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain KA [auth C] Focus chain RA [auth D] Focus chain W [auth B] Interactions & Density Focus chain J [auth A] Focus chain KA [auth C] Focus chain RA [auth D] Focus chain W [auth B]