MolNFT v1 · #157079 · protein

Crystal structure of yersinia pestis udp-glucose pyrophosphorylase

6MNU · UTP--glucose-1-phosphate uridylyltransferase: “Crystal structure of yersinia pestis udp-glucose pyrophosphorylase”. X-ray diffraction, 13 pockets (best druggability 0.87). MolNFT v1 #157079 on GenesisL1: 3D structure, binding sites…

PDB: 6MNU
Type: protein
Length: 1,156 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UTP--glucose-1-phosphate uridylyltransferase
EC: 2.7.7.9
UniProt: A0A2S9PFH5
Pockets: 13 · best druggability 0.87

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)	protein	289	37% helix, 22% strand	A0A2S9PFH5
B	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)	protein	288	37% helix, 22% strand	A0A2S9PFH5
C	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)	protein	292	38% helix, 22% strand	A0A2S9PFH5
D	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9)	protein	287	37% helix, 22% strand	A0A2S9PFH5

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 2 copies · chains B, C, D

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

Pockets

13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1083	0.87	0.88	87	empty
2	890	0.72	0.77	86	empty
3	811	0.70	0.76	71	empty
4	827	0.70	0.76	67	empty
5	777	0.69	0.76	77	empty

Interfaces

6 interfaces between chains.

C–D · 2284 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2129 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 866 Å² buried · 21 hydrogen bonds · protein-protein
B–C · 860 Å² buried · 19 hydrogen bonds · protein-protein
B–D · 162 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6MNU · Crystal structure of Yersinia pestis UDP-glucose pyrophosphorylase · the same entry in another collection · 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 A0A2S9PFH5
Elsewhere: RCSB PDB 6MNU · PDBe 6MNU · UniProt A0A2S9PFH5

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