MolNFT v1 · #106318 · protein
Crystal structure of a putative acyl-CoA ligase (BT_0428) from bacteroides thetaiotaomicron vpi-5482 at 2.20 a resolution
4RVN · Phenylacetate-coenzyme a ligase: “Crystal structure of a putative acyl-CoA ligase (BT_0428) from bacteroides thetaiotaomicron vpi-5482 at 2.20…”. X-ray diffraction, 6 ligands (AMP, UNL, COA), 18 pockets (best druggability 0.83).…
- PDB
- 4RVN
- Type
- protein
- Length
- 1,717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetate-coenzyme a ligase
- UniProt
- Q8AAN6
- Ligands
- AMP, UNL, COA, K, ZN, SO4
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 25% 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 | 424 | 34% helix, 25% strand | Q8AAN6 |
| C | Phenylacetate-coenzyme a ligase | protein | 434 | 33% helix, 25% strand | Q8AAN6 |
| D | Phenylacetate-coenzyme a ligase | protein | 426 | 34% helix, 24% strand | Q8AAN6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 4 copies · chains A, B, C, D
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- 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 · 5 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.83 | 0.88 | 92 | AMP, K, UNL |
| 2 | 1192 | 0.81 | 0.82 | 120 | AMP, COA, K, UNL |
| 3 | 957 | 0.78 | 0.81 | 97 | AMP, UNL, SO4 |
| 4 | 368 | 0.75 | 0.86 | 54 | AMP, UNL |
| 5 | 288 | 0.63 | 0.80 | 46 | SO4 |
Interfaces
4 interfaces between chains.
- A–B · 1827 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1822 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 468 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 444 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 modified (engineered).
Compared structures
- 4RVN · 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 4RVN · PDBe 4RVN · UniProt Q8AAN6
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