Research workbench

E. cloacae mura in complex with udp-glucose

Analyse E. cloacae mura in complex with udp-glucose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4E7B
Type: protein
Length: 1,676 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-N-acetylglucosamine 1-carboxyvinyltransferase
EC: 2.5.1.7
UniProt: P33038
Ligands: UPG
Pockets: 17 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7)	protein	419	36% helix, 27% strand	P33038

Ligands and binding sites

UPG · Uridine-5'-diphosphate-glucose · ligand · 4 copies · chains A, B, C, D
EDO · 1,2-ethanediol · additive · 42 copies · chains A, B, C, D
ACT · Acetate ion · additive · 2 copies · chains A, C

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

Pockets

17 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	1103	0.80	0.82	113	EDO, UPG
2	604	0.79	0.85	71	EDO
3	722	0.77	0.82	83	EDO
4	501	0.73	0.82	77	EDO
5	157	0.65	0.86	22	empty

Interfaces

6 interfaces between chains.

B–C · 882 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 805 Å² buried · 15 hydrogen bonds · protein-protein
A–D · 785 Å² buried · 13 hydrogen bonds · protein-protein
B–D · 754 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 402 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

4E7B · E. cloacae MurA in complex with UDP-glucose · the same entry in another collection · chain A against A, TM-score 1.00
P33038 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.94

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 P33038
Elsewhere: RCSB PDB 4E7B · PDBe 4E7B · UniProt P33038

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