Research workbench

Pamurf in complex with udp-murnac-tripeptide (mdap)

Analyse Pamurf in complex with udp-murnac-tripeptide (mdap) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4CVK
Type: protein
Length: 438 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
EC: 6.3.2.10
UniProt: Q9HVZ7
Ligands: ALA, UDP, MUB, FGA, API
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase (EC 6.3.2.10)	protein	438	37% helix, 22% strand	Q9HVZ7

Ligands and binding sites

ALA · Alanine · ligand · chains A
UDP · Uridine-5'-diphosphate · ligand · chains A
MUB · N-acetyl-alpha-muramic acid · ligand · chains A
FGA · Gamma-D-glutamic acid · ligand · chains A
API · 2,6-diaminopimelic acid · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	341	0.56	0.75	37	empty
2	90	0.38	0.76	19	UDP

Compared structures

4CVK · PaMurF in complex with UDP-MurNAc-tripeptide (mDAP) · the same entry in another collection · chain A against A, TM-score 1.00

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 Q9HVZ7
Elsewhere: RCSB PDB 4CVK · PDBe 4CVK · UniProt Q9HVZ7

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