Research workbench
O-succinylbenzoate CoA synthetase (mene) from bacillus subtilis in complex with the acyl-adenylate intermediate osb-AMP
Analyse O-succinylbenzoate CoA synthetase (mene) from bacillus subtilis in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GTD
- Type
- protein
- Length
- 864 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
- A, OSB, MG, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 484 | 31% helix, 29% strand | P23971 |
| B | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 380 | 33% helix, 28% strand | P23971 |
Ligands and binding sites
- A · Adenosine-5'-monophosphate · ligand · 2 copies · chains A, B
- OSB · 2-succinylbenzoate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A, B
- CL · Chloride ion · ion · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A, B
- IMD · Imidazole · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.80 | 0.82 | 100 | A, OSB |
| 2 | 610 | 0.70 | 0.78 | 81 | A, OSB |
| 3 | 54 | 0.66 | 0.95 | 20 | empty |
| 4 | 244 | 0.63 | 0.81 | 38 | CL |
| 5 | 408 | 0.61 | 0.76 | 46 | empty |
Interfaces
1 interface between chains.
- A–B · 1215 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5GTD · o-Succinylbenzoate CoA Synthetase (MenE) from Bacillus Subtilis in Complex with the… · 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 B against A, TM-score 0.99
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 5GTD · PDBe 5GTD · UniProt P23971
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