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Crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase

Analyse Crystal structures of transition state analogue inhibitors of inosine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2B1G
Type: protein
Length: 2,360 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Bifunctional purine biosynthesis protein purh
EC: 3.5.4.10, 2.1.2.3
UniProt: P31335
Ligands: 13A, K, PO4
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Bifunctional purine biosynthesis protein purh (EC 3.5.4.10, 2.1.2.3)	protein	590	44% helix, 19% strand	P31335

Ligands and binding sites

13A · 7-(3,4-dihydroxy-5R-hydroxymethyltetrahydrofuran-2-yl)-2,2-dioxo-1,2R,3R,7-tetrahydro-2L6-imidazo[4,5-C][1,2, 6]thiadiazin-4S-one · ligand · 2 copies · chains A, B, C, D
K · Potassium ion · metal · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 2 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, 15 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	238	0.84	0.97	47	empty
2	125	0.79	0.97	27	empty
3	1014	0.78	0.80	99	empty
4	115	0.78	0.97	25	empty
5	1088	0.76	0.79	79	empty

Interfaces

3 interfaces between chains.

C–D · 6186 Å² buried · 92 hydrogen bonds · protein-protein
A–B · 6159 Å² buried · 90 hydrogen bonds · protein-protein
B–C · 303 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

2B1G · Crystal structures of transition state analogue inhibitors of inosine monophosphate… · the same entry in another collection · chain A against A, TM-score 1.00
P31335 · AlphaFold monomer V2.0 prediction for bifunctional purine biosynthesis protein atic… · a predicted model of the same protein · chain A against A, TM-score 1.00

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 P31335
Elsewhere: RCSB PDB 2B1G · PDBe 2B1G · UniProt P31335

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