MolNFT v1 · #56021 · protein

Mura inhibited by unag-cnicin adduct

2Z2C · Udp-N-acetylglucosamine 1-carboxyvinyltransferase: “Mura inhibited by unag-cnicin adduct”. X-ray diffraction, 2 ligands (UDP, UDC), 15 pockets (best druggability 0.87). MolNFT v1 #56021 on GenesisL1: 3D structure, binding sites and…

PDB: 2Z2C
Type: protein
Length: 1,672 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: P0A749
Ligands: UDP, UDC
Pockets: 15 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 36% 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	418	36% helix, 28% strand	P0A749

Ligands and binding sites

UDP · Uridine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
UDC · 2-acetamido-3-O-[(2S,3S)-2-carboxy-3,4-dihydroxybutan-2-yl]-2-deoxy-alpha-D-glucopyranose · ligand · 4 copies · chains A, B, C, D

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

Pockets

15 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	760	0.87	0.90	105	UDP, UDC
2	523	0.84	0.90	65	UDP, UDC
3	439	0.84	0.91	56	UDP, UDC
4	438	0.82	0.90	56	UDP, UDC
5	100	0.62	0.88	23	empty

Interfaces

6 interfaces between chains.

A–B · 1175 Å² buried · 9 hydrogen bonds · protein-protein
C–D · 1110 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 840 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 752 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 459 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nonstandard).

Compared structures

2Z2C · MURA inhibited by unag-cnicin adduct · the same entry in another collection · chain A against A, TM-score 1.00
P0A749 · AlphaFold monomer V2.0 prediction for udp-N-acetylglucosamine 1-carboxyvinyltransferase… · a predicted model of the same protein · chain A against A, TM-score 0.99

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 P0A749
Elsewhere: RCSB PDB 2Z2C · PDBe 2Z2C · UniProt P0A749

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