Research workbench
Crystal structure of mure ligase from thermotoga maritima in complex with ADP
Analyse Crystal structure of mure ligase from thermotoga maritima in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BUB
- Type
- protein
- Length
- 961 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--ld-lysine ligase
- EC
- 6.3.2.37, 6.3.2.7
- UniProt
- Q9WY79
- Ligands
- ADP, MG
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--ld-lysine ligase (EC 6.3.2.37, 6.3.2.7) | protein | 478 | 31% helix, 22% strand | Q9WY79 |
| B | Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--ld-lysine ligase (EC 6.3.2.37, 6.3.2.7) | protein | 483 | 34% helix, 23% strand | Q9WY79 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 585 | 0.80 | 0.86 | 73 | ADP |
| 2 | 698 | 0.72 | 0.79 | 77 | ADP, MG |
| 3 | 222 | 0.60 | 0.81 | 40 | empty |
| 4 | 134 | 0.56 | 0.82 | 25 | empty |
| 5 | 157 | 0.54 | 0.80 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 655 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 4BUB · Crystal structure of mure ligase from thermotoga maritima in complex with ADP · the same entry in another collection · chain A against A, TM-score 1.00
- Q9WY79 · AlphaFold monomer V2.0 prediction for udp-N-acetylmuramoyl-L-alanyl… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q9WY79
- Elsewhere: RCSB PDB 4BUB · PDBe 4BUB · UniProt Q9WY79
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