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C115S mura liganded with reaction products

Analyse C115S mura liganded with reaction products in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1RYW
Type: protein
Length: 3,352 residues
Chains: 8
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: EPU, PO4
Pockets: 20 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 34% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Udp-N-acetylglucosamine 1-carboxyvinyltransferase (EC 2.5.1.7)	protein	419	34% helix, 28% strand	P33038

Ligands and binding sites

EPU · Uridine-diphosphate-2(N-acetylglucosaminyl) butyric acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
PO4 · Phosphate ion · ion · 9 copies · chains A, B, C, D, E, F, G, H
GOL · Glycerol · additive · 17 copies · chains A, B, C, D, E, F, G, H

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1150	0.88	0.90	145	PO4, EPU, GOL
2	648	0.86	0.90	93	PO4, EPU, GOL
3	648	0.85	0.90	91	PO4, EPU, GOL
4	574	0.85	0.90	75	PO4, EPU, GOL
5	525	0.84	0.90	64	PO4, EPU, GOL

Interfaces

15 interfaces between chains.

B–D · 1134 Å² buried · 10 hydrogen bonds · protein-protein
G–H · 1118 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 1094 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 1093 Å² buried · 8 hydrogen bonds · protein-protein
F–H · 953 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (nonstandard).

Compared structures

1RYW · C115S MurA liganded with reaction products · the same entry in another collection · chain E against E, 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 0.99

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 P33038
Elsewhere: RCSB PDB 1RYW · PDBe 1RYW · UniProt P33038

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