Research workbench

Mura dead-end complex with terreic acid

Analyse Mura dead-end complex with terreic acid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3KQA
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: TR9, CA
Pockets: 13 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 35% 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	35% helix, 27% strand	P33038

Ligands and binding sites

TR9 · (5S)-2,5-dihydroxy-3-methylcyclohex-2-ene-1,4-dione · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 10 copies · chains A, B, C, D

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

Pockets

13 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	381	0.69	0.81	57	empty
2	353	0.66	0.80	51	empty
3	382	0.66	0.79	57	empty
4	282	0.64	0.81	50	empty
5	208	0.59	0.81	37	empty

Interfaces

3 interfaces between chains.

A–B · 806 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 741 Å² buried · 20 hydrogen bonds · protein-protein
A–C · 216 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).

Compared structures

3KQA · MurA dead-end complex with terreic acid · 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 3KQA · PDBe 3KQA · UniProt P33038

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