Research workbench

Unliganded E.CLOACAE C115D mura

Analyse Unliganded E.CLOACAE C115D mura in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3V5V
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
Pockets: 18 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 26% 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, 26% strand	P33038

Ligands and binding sites

EDO · 1,2-ethanediol · additive · 33 copies · chains A, B, C, D
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, C, D
ACT · Acetate ion · additive · 2 copies · chains A, C, D
PGE · Triethylene glycol · additive · chains B

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

Pockets

18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	956	0.76	0.79	113	EDO
2	487	0.72	0.81	64	EDO
3	480	0.68	0.79	67	PGE, EDO
4	340	0.68	0.82	52	empty
5	455	0.67	0.79	59	empty

Interfaces

6 interfaces between chains.

B–D · 1185 Å² buried · 16 hydrogen bonds · protein-protein
A–C · 1119 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 812 Å² buried · 12 hydrogen bonds · protein-protein
A–D · 545 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 538 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

3V5V · Unliganded E.CLOACAE C115D mura · 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 0.95

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 3V5V · PDBe 3V5V · UniProt P33038

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