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Structure of human guanosine monophosphate reductase GMPR1 in complex with gmp

Analyse Structure of human guanosine monophosphate reductase GMPR1 in complex with gmp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2BWG
Type: protein
Length: 1,321 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gmp reductase I
EC: 1.7.1.7
UniProt: P36959
Ligands: 5GP, K
Pockets: 14 · best druggability 0.82

Structure

x-ray diffraction · 3 distinct chains · 38% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gmp reductase I (EC 1.7.1.7)	protein	335	39% helix, 24% strand	P36959
B, C	Gmp reductase I (EC 1.7.1.7)	protein	329	38% helix, 23% strand	P36959
D	Gmp reductase I (EC 1.7.1.7)	protein	328	38% helix, 24% strand	P36959

Ligands and binding sites

5GP · Guanosine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
K · Potassium 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	182	0.82	0.97	42	5GP
2	208	0.81	0.95	43	5GP
3	373	0.77	0.87	69	5GP
4	438	0.76	0.85	86	5GP
5	224	0.53	0.77	45	empty

Interfaces

4 interfaces between chains.

A–B · 1570 Å² buried · 27 hydrogen bonds · protein-protein
A–C · 1444 Å² buried · 22 hydrogen bonds · protein-protein
C–D · 1436 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 1400 Å² buried · 24 hydrogen bonds · protein-protein

Compared structures

2BWG · Structure of human guanosine monophosphate reductase GMPR1 in complex with GMP · the same entry in another collection · chain A against A, TM-score 1.00
P36959 · AlphaFold monomer V2.0 prediction for gmp reductase 1 (P36959) · 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 P36959
Elsewhere: RCSB PDB 2BWG · PDBe 2BWG · UniProt P36959

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