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Holo IDO1 crystal structure

Analyse Holo IDO1 crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6AZU
Type: protein
Length: 1,472 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Indoleamine 2,3-dioxygenase 1
EC: 1.13.11.52
UniProt: P14902
Ligands: HEM, SO4
Pockets: 20 · best druggability 0.80

Structure

x-ray diffraction · 3 distinct chains · 60% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52)	protein	370	58% helix, 4% strand	P14902
B	Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52)	protein	366	60% helix, 4% strand	P14902
C	Indoleamine 2,3-dioxygenase 1 (EC 1.13.11.52)	protein	366	60% helix, 4% strand	P14902

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1068	0.80	0.81	87	empty
2	584	0.79	0.84	54	HEM
3	614	0.78	0.83	53	HEM
4	644	0.78	0.83	60	HEM
5	619	0.77	0.83	54	HEM

Interfaces

4 interfaces between chains.

A–B · 820 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 458 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 419 Å² buried · 2 hydrogen bonds · protein-protein
C–D · 192 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

6AZU · Holo IDO1 crystal structure · the same entry in another collection · chain A against A, TM-score 1.00
P14902 · AlphaFold monomer V2.0 prediction for indoleamine 2,3-dioxygenase 1 (P14902) · a predicted model of the same protein · chain B against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P14902
Elsewhere: RCSB PDB 6AZU · PDBe 6AZU · UniProt P14902

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