MolNFT v1 · #90045 · protein

E. cloacae C115D mura in complex with udp

4E7F · Udp-N-acetylglucosamine 1-carboxyvinyltransferase: “E. cloacae C115D mura in complex with udp”. X-ray diffraction, 1 ligand (UDP), 19 pockets (best druggability 0.79). MolNFT v1 #90045 on GenesisL1: 3D structure, binding sites and…

PDB: 4E7F
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: 19 · best druggability 0.79

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 · 15 copies · chains A, B, C, D
ACT · Acetate ion · additive · chains C

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

Pockets

19 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	1101	0.79	0.80	108	EDO
2	434	0.73	0.83	67	EDO
3	260	0.72	0.87	46	empty
4	544	0.70	0.79	71	empty
5	501	0.68	0.79	56	empty

Interfaces

6 interfaces between chains.

B–C · 950 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 922 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 802 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 689 Å² buried · 2 hydrogen bonds · protein-protein
B–D · 580 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

4E7F · E. cloacae C115D 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 4E7F · PDBe 4E7F · UniProt P33038

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