MolNFT v1 · #119103 · protein
Crystal structure of the 6-carboxyhexanoate-CoA ligase (BIOW)FROM bacillus subtilis (PTCL4 derivative)
5FM0 · 6-carboxyhexanoate--CoA ligase: “Crystal structure of the 6-carboxyhexanoate-CoA ligase (BIOW)FROM bacillus subtilis (PTCL4 derivative)”. X-ray diffraction, 4 ligands (WAQ, PPV, PT), 5 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 5FM0
- Type
- protein
- Length
- 494 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
- WAQ, PPV, PT, MG
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-carboxyhexanoate--CoA ligase (EC 6.2.1.14) | protein | 247 | 34% helix, 29% strand | P53559 |
| B | 6-carboxyhexanoate--CoA ligase (EC 6.2.1.14) | protein | 247 | 32% helix, 30% strand | P53559 |
Ligands and binding sites
- WAQ · Pimeloyl-amp · ligand · 2 copies · chains A, B
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- PT · Platinum (II) ion · metal · 6 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.80 | 0.88 | 58 | WAQ, PPV |
| 2 | 421 | 0.79 | 0.88 | 61 | WAQ, PPV, MG |
| 3 | 190 | 0.52 | 0.78 | 29 | empty |
| 4 | 133 | 0.52 | 0.81 | 24 | empty |
| 5 | 52 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5FM0 · Crystal structure of the 6-carboxyhexanoate-CoA ligase (BioW)from Bacillus subtilis… · 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 5FM0 · PDBe 5FM0 · UniProt P53559
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