MolNFT v1 · #113106 · protein
Crystal structure of murd ligase from escherichia COLI in complex with uma and ADP
5A5F · Udp-N-acetylmuramoylalanine--D-glutamate ligase: “Crystal structure of murd ligase from escherichia COLI in complex with uma and ADP”. X-ray diffraction, 2 ligands (UMA, ADP), 3 pockets (best druggability 0.72). MolNFT v1 #113106 on…
- PDB
- 5A5F
- Type
- protein
- Length
- 433 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoylalanine--D-glutamate ligase
- EC
- 6.3.2.9
- UniProt
- P14900
- Ligands
- UMA, ADP
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 433 | 36% helix, 22% strand | P14900 |
Ligands and binding sites
- UMA · Uridine-5'-diphosphate-N-acetylmuramoyl-L-alanine · ligand · chains A
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MLI · Malonate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.72 | 0.81 | 70 | UMA, ADP |
| 2 | 189 | 0.50 | 0.77 | 30 | MLI |
| 3 | 66 | 0.29 | 0.73 | 13 | empty |
Compared structures
- 5A5F · Crystal structure of murd ligase from escherichia COLI in complex with uma and ADP · the same entry in another collection · chain A against A, TM-score 1.00
- P14900 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoylalanine-- D-glutamate ligase… · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P14900
- Elsewhere: RCSB PDB 5A5F · PDBe 5A5F · UniProt P14900
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