Research workbench
Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1 in complex with phosphate and ADP
Analyse Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YB8
- Type
- protein
- Length
- 1,386 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 acetyl-coenzyme a…
- UniProt
- B1L3C9, B1L7P8
- Ligands
- ADP, NA, MG, PO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Alpha subunit of acyl-CoA synthetase (ndp forming) | protein | 464 | 44% helix, 19% strand | B1L3C9 |
| B, D | Beta subunit of acetyl-coenzyme a synthetase (dinucleotide- forming) 3 | protein | 229 | 37% helix, 29% strand | B1L7P8 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 3 copies · chains A, C
- MG · Magnesium ion · metal · 2 copies · chains B, D
- PO4 · Phosphate ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.78 | 0.81 | 86 | PO4, NA |
| 2 | 833 | 0.77 | 0.80 | 89 | PO4 |
| 3 | 990 | 0.73 | 0.76 | 81 | empty |
| 4 | 467 | 0.71 | 0.81 | 45 | empty |
| 5 | 61 | 0.56 | 0.89 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2059 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 812 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 793 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 536 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YB8 · Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in… · the same entry in another collection · chain C against C, 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 4YB8 · PDBe 4YB8 · UniProt B1L3C9 · UniProt B1L7P8
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