Research workbench
Crystal structure of a putative acyl-CoA ligase (BT_0428) from bacteroides thetaiotaomicron vpi-5482 at 2.48 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
- 4R1M
- Type
- protein
- Length
- 1,720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phenylacetate-coenzyme a ligase
- UniProt
- Q8AAN6
- Ligands
- AMP, ZN, NA, CL
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phenylacetate-coenzyme a ligase | protein | 435 | 34% helix, 25% strand | Q8AAN6 |
| B | Phenylacetate-coenzyme a ligase | protein | 426 | 35% helix, 25% strand | Q8AAN6 |
| C | Phenylacetate-coenzyme a ligase | protein | 431 | 34% helix, 25% strand | Q8AAN6 |
| D | Phenylacetate-coenzyme a ligase | protein | 428 | 34% helix, 24% strand | Q8AAN6 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, D
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains C
- EDO · 1,2-ethanediol · additive · 15 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.83 | 0.84 | 108 | AMP, EDO |
| 2 | 987 | 0.82 | 0.83 | 99 | empty |
| 3 | 470 | 0.74 | 0.83 | 56 | AMP |
| 4 | 565 | 0.73 | 0.81 | 63 | AMP |
| 5 | 195 | 0.62 | 0.83 | 41 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1836 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1831 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 610 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 554 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 58 modified (engineered).
Compared structures
- 4R1M · 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 4R1M · PDBe 4R1M · UniProt Q8AAN6
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