Research workbench
O-succinylbenzoate coenzyme a synthetase (mene) from bacillus subtilis, in complex with AMP
Analyse O-succinylbenzoate coenzyme a synthetase (mene) from bacillus subtilis, in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BUS
- Type
- protein
- Length
- 862 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-succinylbenzoate--CoA ligase
- EC
- 6.2.1.26
- UniProt
- P23971
- Ligands
- AMP, CL
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 481 | 33% helix, 28% strand | P23971 |
| B | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 381 | 34% helix, 29% strand | P23971 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1061 | 0.79 | 0.81 | 95 | AMP |
| 2 | 485 | 0.68 | 0.79 | 79 | AMP |
| 3 | 311 | 0.67 | 0.81 | 38 | empty |
| 4 | 249 | 0.64 | 0.82 | 42 | CL |
| 5 | 422 | 0.60 | 0.76 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 1195 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- P23971 · AlphaFold monomer V2.0 prediction for 2-succinylbenzoate--CoA ligase (P23971) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P23971
- Elsewhere: RCSB PDB 5BUS · PDBe 5BUS · UniProt P23971
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