MolNFT v1 · #137038 · protein
Crystal structure of holo-[acyl-carrier-protein] synthase (acps) from escherichia COLI
5VBX: “Crystal structure of holo-[acyl-carrier-protein] synthase (acps) from escherichia COLI”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.46). MolNFT v1 #137038 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5VBX
- Type
- protein
- Length
- 375 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
- NA
- Pockets
- 6 · best druggability 0.46
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 125 | 45% helix, 30% strand | P24224 |
Ligands and binding sites
- NA · Sodium ion · metal · 9 copies · chains A, C, B
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.46 | 0.74 | 37 | EDO |
| 2 | 160 | 0.42 | 0.74 | 36 | EDO |
| 3 | 131 | 0.41 | 0.75 | 35 | EDO |
| 4 | 72 | 0.37 | 0.77 | 16 | EDO |
| 5 | 59 | 0.33 | 0.77 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–C · 798 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 777 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 760 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5VBX · Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Escherichia coli · 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 A 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 P24224
- Elsewhere: RCSB PDB 5VBX · PDBe 5VBX · UniProt P24224
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