MolNFT v1 · #87218 · protein
Crystal structure of mure ligase from thermotoga maritima in complex with ADP
4BUB · Udp-N-acetylmuramoyl-L-alanyl-D-glutamate--ld-lysine ligase: “Crystal structure of mure ligase from thermotoga maritima in complex with ADP”. X-ray diffraction, 2 ligands (ADP, MG), 9 pockets (best druggability 0.80). MolNFT v1…
- 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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