MolNFT v1 · #115902 · protein
1.75 ångström resolution crystal structure of the apo-form acyl- carrier-protein synthase (acps) (acps; purification tag off) from staphylococcus aureus subsp. aureus col in the I4 space group
5CXD · Holo-[acyl-carrier-protein] synthase: “1.75 ångström resolution crystal structure of the apo-form acyl- carrier-protein synthase (acps) (acps…”. X-ray diffraction, 2 ligands (NI, CL), 5 pockets (best druggability 0.53). MolNFT v1…
- PDB
- 5CXD
- Type
- protein
- Length
- 362 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
- Q5HED0
- Ligands
- NI, CL
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 119 | 42% helix, 28% strand | Q5HED0 |
| B | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 122 | 43% helix, 29% strand | Q5HED0 |
| C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 121 | 40% helix, 27% strand | Q5HED0 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains C
- CL · Chloride ion · ion · 12 copies · chains A, B, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.53 | 0.76 | 49 | CL |
| 2 | 114 | 0.47 | 0.80 | 20 | CL |
| 3 | 163 | 0.45 | 0.75 | 27 | CL |
| 4 | 67 | 0.37 | 0.78 | 16 | empty |
| 5 | 66 | 0.32 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 952 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 893 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 781 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5CXD · 1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HED0 · AlphaFold monomer V2.0 prediction for holo-[acyl-carrier-protein] synthase (Q5HED0) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q5HED0
- Elsewhere: RCSB PDB 5CXD · PDBe 5CXD · UniProt Q5HED0
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