Research workbench
Unliganded form of O-succinylbenzoate coenzyme a synthetase (mene) from bacillus subtilis, solved at 1.98 ångströms
Analyse Unliganded form of O-succinylbenzoate coenzyme a synthetase (mene) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BUQ
- Type
- protein
- Length
- 927 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
- CA
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 454 | 33% helix, 28% strand | P23971 |
| B | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 473 | 33% helix, 28% strand | P23971 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 456 | 0.63 | 0.77 | 50 | empty |
| 2 | 491 | 0.63 | 0.76 | 73 | empty |
| 3 | 248 | 0.63 | 0.81 | 36 | ACT |
| 4 | 194 | 0.62 | 0.83 | 36 | empty |
| 5 | 218 | 0.56 | 0.79 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 1237 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5BUQ · Unliganded Form of O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P23971 · AlphaFold monomer V2.0 prediction for 2-succinylbenzoate--CoA ligase (P23971) · a predicted model of the same protein · chain A against A, TM-score 0.86
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 5BUQ · PDBe 5BUQ · UniProt P23971
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