MolNFT v1 · #122562 · protein
Structure of the holo pcp-E didomain of the gramicidin S synthetase a
5ISX · Gramicidin S synthase 1: “Structure of the holo pcp-E didomain of the gramicidin S synthetase a”. X-ray diffraction, 1 ligand (PNS), 14 pockets (best druggability 0.84). MolNFT v1 #122562 on GenesisL1: 3D structure, binding sites…
- PDB
- 5ISX
- Type
- protein
- Length
- 1,058 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gramicidin S synthase 1
- EC
- 5.1.1.11
- UniProt
- P0C062
- Ligands
- PNS
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gramicidin S synthase 1 (EC 5.1.1.11) | protein | 529 | 40% helix, 19% strand | P0C062 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 744 | 0.84 | 0.87 | 100 | PNS |
| 2 | 598 | 0.82 | 0.87 | 73 | PNS |
| 3 | 761 | 0.72 | 0.78 | 74 | empty |
| 4 | 52 | 0.68 | 0.97 | 17 | empty |
| 5 | 316 | 0.63 | 0.79 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 702 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (phosphopantetheinylation).
Compared structures
- 5ISX · Structure of the holo PCP-E didomain of the gramicidin S synthetase A · the same entry in another collection · chain A against A, TM-score 1.00
- P0C062 · AlphaFold monomer V2.0 prediction for gramicidin S synthase 1 (P0C062) · 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 P0C062
- Elsewhere: RCSB PDB 5ISX · PDBe 5ISX · UniProt P0C062
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