7Z2L | pdb_00007z2l

Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1)

PDB DOI: https://doi.org/10.2210/pdb7Z2L/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2022-02-28 Released: 2023-03-22
Deposition Author(s): Mirgaux, M., Wouters, J.
Funding Organization(s): Fonds de la Recherche Scientifique (FNRS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.56 Å
R-Value Free:
0.244 (Depositor), 0.245 (DCC)
R-Value Work:
0.180 (Depositor), 0.182 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of L-Kynurenine in the active site of human Indoleamine-2,3-dioxygenase 1 (hIDO1)

Mirgaux, M., Wouters, J.

To be published.

Macromolecule Content

Total Structure Weight: 185.95 kDa
Atom Count: 13,073
Modeled Residue Count: 1,496
Deposited Residue Count: 1,620
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Indoleamine 2,3-dioxygenase 1	A, B, C, D	405	Homo sapiens	Mutation(s): 2 Gene Names: IDO1, IDO, INDO EC: 1.13.11.52
UniProt & NIH Common Fund Data Resources
Find proteins for P14902 (Homo sapiens) Explore P14902 Go to UniProtKB: P14902
PHAROS: P14902 GTEx: ENSG00000131203
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P14902
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM (Subject of Investigation/LOI) Query on HEM Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain Y [auth D] SDF format, chain L [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain L [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth C] mmCIF format, chain Y [auth D] mmCIF format, chain L [auth B] mmCIF format, chain E [auth A]	E [auth A], L [auth B], S [auth C], Y [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Y [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain S [auth C] Focus chain Y [auth D]
KYN (Subject of Investigation/LOI) Query on KYN Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	J [auth A], M [auth B], N [auth B], P [auth B]	(2S)-2-amino-4-(2-aminophenyl)-4-oxobutanoic acid C₁₀ H₁₂ N₂ O₃ YGPSJZOEDVAXAB-QMMMGPOBSA-N		Interactions Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B] Interactions & Density Focus chain J [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain X [auth C] SDF format, chain Z [auth D] SDF format, chain W [auth C] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain H [auth A] SDF format, chain F [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain X [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain W [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain F [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain X [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain W [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain H [auth A] mmCIF format, chain F [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] CA [auth D] F [auth A] G [auth A] AA [auth D], BA [auth D], CA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], K [auth A], O [auth B], R [auth B], T [auth C], U [auth C], W [auth C], X [auth C], Z [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Z [auth D]
OXY Query on OXY Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth B]	Q [auth B], V [auth C]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain Q [auth B] Focus chain V [auth C] Interactions & Density Focus chain Q [auth B] Focus chain V [auth C]