MolNFT v1 · #110510 · protein
Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1 (se-met derivative) in complex with coenzyme a and mg- amppcp, phosphohistidine segment pointing towards nucleotide binding site
4XZ3 · Acyl-CoA synthetase (ndp forming): “Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1 (se-met derivative) in…”. X-ray diffraction, 3 ligands (ACP, COA, MG), 16 pockets (best druggability 0.72). MolNFT…
- PDB
- 4XZ3
- Type
- protein
- Length
- 1,365 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-CoA synthetase (ndp forming); Uncharacterized protein
- UniProt
- B1L3C9, B1L7P8
- Ligands
- ACP, COA, MG
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acyl-CoA synthetase (ndp forming) | protein | 463 | 42% helix, 18% strand | B1L3C9 |
| B | Uncharacterized protein | protein | 228 | 38% helix, 29% strand | B1L7P8 |
| C | Acyl-CoA synthetase (ndp forming) | protein | 461 | 43% helix, 18% strand | B1L3C9 |
| D | Uncharacterized protein | protein | 213 | 38% helix, 27% strand | B1L7P8 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, C, B, D
- COA · Coenzyme A · ligand · 2 copies · chains A, C
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1105 | 0.72 | 0.76 | 90 | empty |
| 2 | 465 | 0.70 | 0.81 | 47 | empty |
| 3 | 430 | 0.64 | 0.78 | 44 | COA, ACP, MG |
| 4 | 483 | 0.62 | 0.76 | 44 | ACP, MG |
| 5 | 362 | 0.61 | 0.77 | 41 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1703 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1299 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1239 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 538 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
- 4XZ3 · Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 (Se-Met… · 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 4XZ3 · PDBe 4XZ3 · UniProt B1L3C9 · UniProt B1L7P8
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