MolNFT v1 · #139921 · protein
Crystal structure of escherichia COLI holo-[acyl-carrier-protein] synthase (acps) D9A mutant in complex with CoA
5XUH: “Crystal structure of escherichia COLI holo-[acyl-carrier-protein] synthase (acps) D9A mutant in complex with…”. X-ray diffraction, 2 ligands (COA, CL), 3 pockets (best druggability 0.44). MolNFT v1 #139921 on GenesisL1: 3D…
- PDB
- 5XUH
- Type
- protein
- Length
- 368 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
- P24224
- Ligands
- COA, CL
- Pockets
- 3 · best druggability 0.44
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 125 | 46% helix, 30% strand | P24224 |
| B | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 118 | 49% helix, 31% strand | P24224 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains B, C, A
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- GOL · Glycerol · additive · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.44 | 0.75 | 25 | COA |
| 2 | 101 | 0.43 | 0.78 | 20 | empty |
| 3 | 119 | 0.39 | 0.75 | 21 | COA |
Interfaces
3 interfaces between chains.
- A–C · 769 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 751 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 711 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5XUH · Crystal structure of Escherichia coli holo-[acyl-carrier-protein] synthase (AcpS) D9A… · the same entry in another collection · chain A against A, TM-score 1.00
- P24224 · AlphaFold monomer V2.0 prediction for holo-[acyl-carrier-protein] synthase (P24224) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P24224
- Elsewhere: RCSB PDB 5XUH · PDBe 5XUH · UniProt P24224
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