Research workbench
Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1 in complex with ADP and with phosphorylated phosphohistidine segment (site I orientation)
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
- 4YBZ
- Type
- protein
- Length
- 1,383 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
- ADP, MG
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha subunit of acyl-CoA synthetase (ndp forming) | protein | 463 | 44% helix, 18% strand | B1L3C9 |
| B, D | Beta subunit of acyl-CoA synthetase (ndp forming) | protein | 229 | 36% helix, 29% strand | B1L7P8 |
| C | Alpha subunit of acyl-CoA synthetase (ndp forming) | protein | 462 | 44% helix, 18% strand | B1L3C9 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains D
- MG · Magnesium ion · metal · 2 copies · chains A, C
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 | 580 | 0.74 | 0.82 | 79 | MG |
| 2 | 1017 | 0.73 | 0.76 | 75 | empty |
| 3 | 420 | 0.72 | 0.82 | 45 | MG |
| 4 | 470 | 0.71 | 0.81 | 42 | empty |
| 5 | 147 | 0.58 | 0.83 | 37 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2119 Ų buried · 29 hydrogen bonds · protein-protein
- C–D · 824 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 758 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 550 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 4YBZ · Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in… · 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 4YBZ · PDBe 4YBZ · UniProt B1L3C9 · UniProt B1L7P8
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