MolNFT v1 · #88463 · protein
Pamurf in complex with AMP-pnp and udp-murnac-tripeptide (mdap)
4CVM · Udp-N-acetylmuramoyl-tripeptide--D-alanyl-D- alanine ligase: “Pamurf in complex with AMP-pnp and udp-murnac-tripeptide (mdap)”. X-ray diffraction, 6 ligands (ALA, UDP, MUB), 2 pockets (best druggability 0.67). MolNFT v1 #88463 on…
- PDB
- 4CVM
- Type
- protein
- Length
- 443 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, ANP, MG
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 36% 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 | 443 | 36% 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
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.67 | 0.76 | 58 | ANP, MG |
| 2 | 90 | 0.39 | 0.77 | 20 | UDP |
Compared structures
- 4CVM · PaMurF in complex with AMP-PNP and 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 4CVM · PDBe 4CVM · UniProt Q9HVZ7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.