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2.31 ångström resolution crystal structure of a holo-(acyl-carrier- protein) synthase from bacillus anthracis str. ames in complex with CoA (3',5'-ADP)
Analyse 2.31 ångström resolution crystal structure of a holo-(acyl-carrier- protein)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HYK
- Type
- protein
- Length
- 348 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Holo-[acyl-carrier-protein] synthase
- EC
- 2.7.8.7
- UniProt
- Q81JG3
- Ligands
- A3P, MG, CL
- Pockets
- 3 · best druggability 0.52
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 117 | 38% helix, 30% strand | Q81JG3 |
| B | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 115 | 38% helix, 30% strand | Q81JG3 |
| C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 116 | 39% helix, 30% strand | Q81JG3 |
Ligands and binding sites
- A3P · Adenosine-3'-5'-diphosphate · ligand · 6 copies · chains A, B, C
- MG · Magnesium ion · metal · 9 copies · chains A, C, B
- CL · Chloride ion · ion · 6 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 206 | 0.52 | 0.77 | 33 | MG, CL, A3P |
| 2 | 181 | 0.49 | 0.76 | 33 | A3P, MG, CL |
| 3 | 197 | 0.49 | 0.76 | 33 | CL, A3P, MG |
Interfaces
3 interfaces between chains.
- A–C · 857 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 788 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 3HYK · 2.31 Angstrom resolution crystal structure of a holo-(acyl-carrier-protein) synthase from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q81JG3 · AlphaFold monomer V2.0 prediction for holo-[acyl-carrier-protein] synthase (Q81JG3) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q81JG3
- Elsewhere: RCSB PDB 3HYK · PDBe 3HYK · UniProt Q81JG3
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