Research workbench
Crystal structure of a putative acyl-CoA ligase (BT_0428) from bacteroides thetaiotaomicron vpi-5482 at 2.42 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
- 4R1L
- Type
- protein
- Length
- 1,714 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetate-coenzyme a ligase
- UniProt
- Q8AAN6
- Ligands
- ADP, AMP, COA, K, ZN, SO4
- Pockets
- 16 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylacetate-coenzyme a ligase | protein | 433 | 33% helix, 25% strand | Q8AAN6 |
| B | Phenylacetate-coenzyme a ligase | protein | 422 | 34% helix, 25% strand | Q8AAN6 |
| C | Phenylacetate-coenzyme a ligase | protein | 434 | 33% helix, 23% strand | Q8AAN6 |
| D | Phenylacetate-coenzyme a ligase | protein | 425 | 34% helix, 24% strand | Q8AAN6 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 3 copies · chains A, B, D
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, C
- COA · Coenzyme A · ligand · 2 copies · chains A, C
- 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 · 12 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.82 | 0.84 | 100 | AMP, COA, K |
| 2 | 1106 | 0.82 | 0.83 | 108 | ADP, AMP, COA, K, PGE, SO4 |
| 3 | 942 | 0.78 | 0.80 | 98 | ADP, SO4, EDO |
| 4 | 734 | 0.78 | 0.82 | 92 | ADP, PEG, SO4 |
| 5 | 244 | 0.52 | 0.76 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1828 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 1802 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 449 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 423 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 modified (engineered).
Compared structures
- 4R1L · 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 4R1L · PDBe 4R1L · UniProt Q8AAN6
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