MolNFT v1 · #87431 · protein
X-ray crystal structure of staphylococcus aureus mure with udp-murnac- ala-glu-lys
4C13 · Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase: “X-ray crystal structure of staphylococcus aureus mure with udp-murnac- ala-glu-lys”. X-ray diffraction, 5 ligands (UML, MG, K), 5 pockets (best druggability 0.79). MolNFT…
- PDB
- 4C13
- Type
- protein
- Length
- 490 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
- D4U2M7
- Ligands
- UML, MG, K, CL, PO4
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 35% 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 | 490 | 35% helix, 25% strand | D4U2M7 |
Ligands and binding sites
- UML · Uridine 5'Diphospho N-acetyl muramoyl-L-Alanyl-D-Glutamyl-L-Lysine · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 802 | 0.79 | 0.83 | 93 | MG, UML, PO4 |
| 2 | 58 | 0.39 | 0.80 | 17 | empty |
| 3 | 59 | 0.39 | 0.80 | 19 | empty |
| 4 | 107 | 0.37 | 0.75 | 19 | empty |
| 5 | 59 | 0.33 | 0.77 | 16 | empty |
Modifications
Observed in the structure: 1 modified (carboxylation).
Compared structures
- 4C13 · x-ray crystal structure of Staphylococcus aureus MurE with UDP-MurNAc- Ala-Glu-Lys · 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 D4U2M7
- Elsewhere: RCSB PDB 4C13 · PDBe 4C13 · UniProt D4U2M7
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