MolNFT v1 · #114608 · protein
O-succinylbenzoate coenzyme a synthetase (mene) from bacillus subtilis, in complex with ATP and magnesium ion
5BUR · 2-succinylbenzoate--CoA ligase: “O-succinylbenzoate coenzyme a synthetase (mene) from bacillus subtilis, in complex with ATP and magnesium ion”. X-ray diffraction, 3 ligands (ATP, MG, CL), 10 pockets (best druggability 0.80). MolNFT…
- PDB
- 5BUR
- Type
- protein
- Length
- 840 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
- ATP, MG, CL
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 475 | 31% helix, 28% strand | P23971 |
| B | 2-succinylbenzoate--CoA ligase (EC 6.2.1.26) | protein | 365 | 30% helix, 27% strand | P23971 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 6 copies · chains A, B
- GOL · Glycerol · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
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 | 1055 | 0.80 | 0.82 | 86 | MG, ATP, EDO |
| 2 | 428 | 0.72 | 0.82 | 46 | empty |
| 3 | 284 | 0.67 | 0.83 | 36 | CL |
| 4 | 374 | 0.66 | 0.80 | 60 | CL |
| 5 | 378 | 0.59 | 0.76 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 1189 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5BUR · O-succinylbenzoate Coenzyme A Synthetase (MenE) from Bacillus Subtilis, in Complex with… · 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 5BUR · PDBe 5BUR · UniProt P23971
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