MolNFT v1 · #115533 · protein
Crystal structure of holo-[acyl-carrier-protein] synthase (acps) from neisseria meningitidis
5CMO: “Crystal structure of holo-[acyl-carrier-protein] synthase (acps) from neisseria meningitidis”. X-ray diffraction, 6 pockets (best druggability 0.52). MolNFT v1 #115533 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CMO
- 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
- A1KVH5
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Holo-[acyl-carrier-protein] synthase (EC 2.7.8.7) | protein | 125 | 44% helix, 32% strand | A1KVH5 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.52 | 0.80 | 26 | empty |
| 2 | 166 | 0.44 | 0.75 | 31 | GOL |
| 3 | 135 | 0.41 | 0.75 | 25 | empty |
| 4 | 51 | 0.37 | 0.81 | 16 | empty |
| 5 | 103 | 0.36 | 0.74 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 813 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 805 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 665 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5CMO · Crystal structure of holo-[acyl-carrier-protein] synthase (AcpS) from Neisseria… · the same entry in another collection · chain A against A, TM-score 1.00
- A1KVH5 · AlphaFold monomer V2.0 prediction for holo-[acyl-carrier-protein] synthase (A1KVH5) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A1KVH5
- Elsewhere: RCSB PDB 5CMO · PDBe 5CMO · UniProt A1KVH5
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