MolNFT v1 · #119611 · protein
Crystal structure of the 6-carboxyhexanoate-CoA ligase (BIOW)FROM bacillus subtilis in complex with coenzyme a
5G1F: “Crystal structure of the 6-carboxyhexanoate-CoA ligase (BIOW)FROM bacillus subtilis in complex with coenzyme a”. X-ray diffraction, 2 ligands (PML, COA), 3 pockets (best druggability 0.82). MolNFT v1 #119611 on GenesisL1: 3D…
- PDB
- 5G1F
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 6-carboxyhexanoate-CoA ligase
- EC
- 6.2.1.14
- UniProt
- P53559
- Ligands
- PML, COA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-carboxyhexanoate-CoA ligase (EC 6.2.1.14) | protein | 245 | 33% helix, 29% strand | P53559 |
| B | 6-carboxyhexanoate-CoA ligase (EC 6.2.1.14) | protein | 248 | 32% helix, 28% strand | P53559 |
Ligands and binding sites
- PML · Pimelic acid · ligand · 2 copies · chains A, B
- COA · Coenzyme A · ligand · chains A, B
- 2PE · Nonaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.82 | 0.88 | 58 | PML |
| 2 | 633 | 0.82 | 0.87 | 62 | PML, 2PE |
| 3 | 68 | 0.28 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 961 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5G1F · Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis in… · the same entry in another collection · chain A against A, TM-score 1.00
- P53559 · AlphaFold monomer V2.0 prediction for 6-carboxyhexanoate--CoA ligase (P53559) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P53559
- Elsewhere: RCSB PDB 5G1F · PDBe 5G1F · UniProt P53559
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