Research workbench
Crystal structure of murd ligase from thermotoga maritima in apo form
Analyse Crystal structure of murd ligase from thermotoga maritima in apo form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BUC
- Type
- protein
- Length
- 854 residues
- Chains
- 2
- 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
- Q9WY76
- Ligands
- PO4, CL, PO3, NH4
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Udp-N-acetylmuramoylalanine--D-glutamate ligase (EC 6.3.2.9) | protein | 427 | 38% helix, 22% strand | Q9WY76 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 16 copies · chains A, B
- CL · Chloride ion · ion · 6 copies · chains A, B
- PO3 · Phosphite ion · ion · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.41 | 0.78 | 20 | empty |
| 2 | 69 | 0.31 | 0.75 | 19 | empty |
| 3 | 72 | 0.29 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 4BUC · Crystal structure of murd ligase from thermotoga maritima in apo form · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WY76 · 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 0.73
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 Q9WY76
- Elsewhere: RCSB PDB 4BUC · PDBe 4BUC · UniProt Q9WY76
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