Research workbench
Crystal structure of a putative acyl-CoA ligase (BT_0428) from bacteroides thetaiotaomicron vpi-5482 at 2.41 a resolution
Analyse Crystal structure of a putative acyl-CoA ligase (BT_0428) from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RVO
- Type
- protein
- Length
- 1,724 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetate-coenzyme a ligase
- UniProt
- Q8AAN6
- Ligands
- ADP, UNL, K, ZN, SO4
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Phenylacetate-coenzyme a ligase | protein | 434 | 33% helix, 25% strand | Q8AAN6 |
| B | Phenylacetate-coenzyme a ligase | protein | 428 | 33% helix, 24% strand | Q8AAN6 |
| D | Phenylacetate-coenzyme a ligase | protein | 428 | 34% helix, 24% strand | Q8AAN6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- K · Potassium ion · metal · 6 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 14 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- PGE · Triethylene glycol · additive · 2 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 872 | 0.83 | 0.85 | 102 | ADP, K, UNL, EDO |
| 2 | 1134 | 0.83 | 0.84 | 124 | ADP, K, UNL, SO4, EDO |
| 3 | 840 | 0.81 | 0.84 | 95 | ADP, UNL, SO4 |
| 4 | 473 | 0.76 | 0.84 | 63 | ADP, UNL |
| 5 | 285 | 0.65 | 0.81 | 50 | SO4 |
Interfaces
4 interfaces between chains.
- C–D · 1834 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 1830 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 590 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 574 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 modified (engineered).
Compared structures
- 4RVO · Crystal structure of a Putative Acyl-CoA ligase (BT_0428) from Bacteroides… · the same entry in another collection · 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 Q8AAN6
- Elsewhere: RCSB PDB 4RVO · PDBe 4RVO · UniProt Q8AAN6
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