Research workbench

E. cloacae mura in complex with udp

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

PDB: 4E7D
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: UDP
Pockets: 17 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 28% 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	34% helix, 28% strand	P33038

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · chains A
EDO · 1,2-ethanediol · additive · 16 copies · chains A, D, B, C
ACT · Acetate ion · additive · 2 copies · chains C, D

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

Pockets

17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	368	0.78	0.88	47	empty
2	402	0.72	0.83	63	empty
3	560	0.72	0.80	53	empty
4	361	0.69	0.82	44	EDO
5	404	0.68	0.81	66	empty

Interfaces

6 interfaces between chains.

A–B · 1037 Å² buried · 13 hydrogen bonds · protein-protein
C–D · 975 Å² buried · 6 hydrogen bonds · protein-protein
A–D · 806 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 643 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 637 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

4E7D · E. cloacae MurA in complex with UDP · 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 4E7D · PDBe 4E7D · UniProt P33038

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