Research workbench
Crystal structure of murd ligase from escherichia COLI in complex with uma and ADP
Analyse Crystal structure of murd ligase from escherichia COLI in complex with uma and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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