MolNFT v1 · #87430 · protein
X-ray crystal structure of staphylococcus aureus mure with udp-murnac-ala-glu-lys and ADP
4C12 · Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase: “X-ray crystal structure of staphylococcus aureus mure with udp-murnac-ala-glu-lys and ADP”. X-ray diffraction, 3 ligands (UML, ADP, MG), 4 pockets (best druggability…
- PDB
- 4C12
- Type
- protein
- Length
- 493 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase
- EC
- 6.3.2.7
- UniProt
- Q2FZP6
- Ligands
- UML, ADP, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase (EC 6.3.2.7) | protein | 493 | 34% helix, 25% strand | Q2FZP6 |
Ligands and binding sites
- UML · Uridine 5'Diphospho N-acetyl muramoyl-L-Alanyl-D-Glutamyl-L-Lysine · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.81 | 0.84 | 98 | UML, ADP, MG |
| 2 | 214 | 0.47 | 0.74 | 28 | UML |
| 3 | 64 | 0.39 | 0.79 | 16 | empty |
| 4 | 54 | 0.33 | 0.77 | 19 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 4C12 · X-ray Crystal Structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q2FZP6 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoyl-L-alanyl… · 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 Q2FZP6
- Elsewhere: RCSB PDB 4C12 · PDBe 4C12 · UniProt Q2FZP6
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