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Crystal structure of the catalytic domain of the inosine monophosphate dehydrogenase from campylobacter jejuni in the complex with inhibitor P182

Analyse Crystal structure of the catalytic domain of the inosine monophosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5UQH
Type: protein
Length: 2,865 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase
EC: 1.1.1.205
UniProt: A0A1B3XFT6, A5KFK9
Ligands: IMP, 8L1, K
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 8 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	368	38% helix, 21% strand	A0A1B3XFT6, A5KFK9
B	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	358	35% helix, 22% strand	A0A1B3XFT6, A5KFK9
C	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	356	37% helix, 21% strand	A0A1B3XFT6, A5KFK9
D	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	355	35% helix, 22% strand	A0A1B3XFT6, A5KFK9
E	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	357	36% helix, 22% strand	A0A1B3XFT6, A5KFK9
F	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	361	36% helix, 22% strand	A0A1B3XFT6, A5KFK9
G	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	354	35% helix, 21% strand	A0A1B3XFT6, A5KFK9
H	Inosine-5'-monophosphate DEHYDROGENASE,INOSINE-5'- monophosphate dehydrogenase (EC 1.1.1.205)	protein	356	36% helix, 22% strand	A0A1B3XFT6, A5KFK9

Ligands and binding sites

IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
8L1 · N-{4-chloro-3-[4-(trifluoromethyl)-1,3-thiazol-2-yl]phenyl}-N'-(2-{3-[(1E)-N-hydroxyethanimidoyl]phenyl}propan-2-yl)urea · ligand · 8 copies · chains A, B, C, D, E, F, G, H
K · Potassium ion · metal · 8 copies · chains A, B, C, D, E, H, F, G
EDO · 1,2-ethanediol · additive · 5 copies · chains D, E, F
IPA · Isopropyl alcohol · additive · chains G

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

Pockets

20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1016	0.81	0.82	96	empty
2	896	0.80	0.82	86	IMP, 8L1
3	891	0.80	0.82	82	IMP, 8L1
4	816	0.79	0.82	77	IMP, 8L1, EDO
5	526	0.78	0.85	60	IMP, 8L1

Interfaces

15 interfaces between chains.

A–B · 2439 Å² buried · 43 hydrogen bonds · protein-protein
A–D · 2424 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 2408 Å² buried · 38 hydrogen bonds · protein-protein
G–H · 2395 Å² buried · 37 hydrogen bonds · protein-protein
E–F · 2395 Å² buried · 44 hydrogen bonds · protein-protein

Compared structures

5UQH · Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt A0A1B3XFT6
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Elsewhere: RCSB PDB 5UQH · PDBe 5UQH · UniProt A0A1B3XFT6 · UniProt A5KFK9

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