Research workbench
Ca. korarchaeum cryptofilum ACD1 in complex with coenzyme a
Analyse Ca. korarchaeum cryptofilum ACD1 in complex with coenzyme a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XYL
- Type
- protein
- Length
- 1,377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha subunit of acyl-CoA synthetase (ndp forming); Beta subunit of acyl-CoA synthetase…
- UniProt
- B1L3C9, B1L7P8
- Ligands
- COA, CL
- Pockets
- 15 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha subunit of acyl-CoA synthetase (ndp forming) | protein | 463 | 43% helix, 18% strand | B1L3C9 |
| B | Beta subunit of acyl-CoA synthetase (ndp forming) | protein | 225 | 38% helix, 29% strand | B1L7P8 |
| D | Beta subunit of acyl-CoA synthetase (ndp forming) | protein | 226 | 37% helix, 29% strand | B1L7P8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.77 | 0.79 | 104 | CL |
| 2 | 830 | 0.76 | 0.80 | 100 | CL |
| 3 | 985 | 0.73 | 0.76 | 79 | empty |
| 4 | 446 | 0.69 | 0.81 | 43 | empty |
| 5 | 147 | 0.53 | 0.80 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–C · 1952 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 823 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 818 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 534 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4XYL · Ca. Korarchaeum cryptofilum ACD1 in complex with coenzyme A · 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 B1L3C9
- Every structure of UniProt B1L7P8
- Elsewhere: RCSB PDB 4XYL · PDBe 4XYL · UniProt B1L3C9 · UniProt B1L7P8
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