MolNFT v1 · #119089 · protein
Crystal structure of the 6-carboxyhexanoate-CoA ligase (biow) from bacillus subtilis in complex with a pimeloyl-adenylate
5FLL: “Crystal structure of the 6-carboxyhexanoate-CoA ligase (biow) from bacillus subtilis in complex with a…”. X-ray diffraction, 3 ligands (WAQ, PPV, MG), 5 pockets (best druggability 0.81). MolNFT v1 #119089 on GenesisL1: 3D structure…
- PDB
- 5FLL
- Type
- protein
- Length
- 502 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, MG
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 6-carboxyhexanoate-CoA ligase (EC 6.2.1.14) | protein | 251 | 32% helix, 29% strand | P53559 |
| B | 6-carboxyhexanoate-CoA ligase (EC 6.2.1.14) | protein | 251 | 34% helix, 29% strand | P53559 |
Ligands and binding sites
- WAQ · Pimeloyl-amp · ligand · 2 copies · chains A, B
- PPV · Pyrophosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
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 | 378 | 0.81 | 0.90 | 51 | WAQ, PPV, MG |
| 2 | 421 | 0.80 | 0.88 | 54 | WAQ, PPV, MG |
| 3 | 225 | 0.56 | 0.79 | 30 | empty |
| 4 | 172 | 0.54 | 0.80 | 23 | empty |
| 5 | 50 | 0.26 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5FLL · 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 A 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 5FLL · PDBe 5FLL · UniProt P53559
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