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Crystal structure of ido from bacillus thuringiensis

Analyse Crystal structure of ido from bacillus thuringiensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6LNH
Type: protein
Length: 887 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-isoleucine-4-hydroxylase
EC: 1.14.11.45
UniProt: E2GIN1
Ligands: HG, FE
Pockets: 14 · best druggability 0.78

Structure

x-ray diffraction · 4 distinct chains · 22% helix, 33% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-isoleucine-4-hydroxylase (EC 1.14.11.45)	protein	225	21% helix, 32% strand	E2GIN1
B	L-isoleucine-4-hydroxylase (EC 1.14.11.45)	protein	223	22% helix, 33% strand	E2GIN1
C	L-isoleucine-4-hydroxylase (EC 1.14.11.45)	protein	228	21% helix, 33% strand	E2GIN1
D	L-isoleucine-4-hydroxylase (EC 1.14.11.45)	protein	211	22% helix, 35% strand	E2GIN1

Ligands and binding sites

HG · Mercury (II) ion · metal · 7 copies · chains A, C, B, D
FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.78	0.80	68	HG
2	141	0.78	0.95	32	empty
3	209	0.72	0.88	31	FE
4	254	0.72	0.87	42	empty
5	321	0.71	0.84	34	FE

Interfaces

4 interfaces between chains.

C–D · 1012 Å² buried · 5 hydrogen bonds · protein-protein
A–B · 991 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 939 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 936 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

6LNH · Crystal structure of IDO from Bacillus thuringiensis · the same entry in another collection · chain D against D, TM-score 1.00
E2GIN1 · AlphaFold monomer V2.0 prediction for L-isoleucine-4-hydroxylase (E2GIN1) · a predicted model of the same protein · chain D 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 E2GIN1
Elsewhere: RCSB PDB 6LNH · PDBe 6LNH · UniProt E2GIN1

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