MolNFT v1 · #180324 · protein
Non-ribosomal didomain (stabilised glycine-pcp-C) acceptor bound state
7KW0 · Pcp-C didomain: “Non-ribosomal didomain (stabilised glycine-pcp-C) acceptor bound state”. X-ray diffraction, 1 ligand (XAG), 10 pockets (best druggability 0.85). MolNFT v1 #180324 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7KW0
- Type
- protein
- Length
- 1,030 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcp-C didomain
- UniProt
- Q47NR9
- Ligands
- XAG
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pcp-C didomain | protein | 514 | 40% helix, 18% strand | Q47NR9 |
| B | Pcp-C didomain | protein | 516 | 41% helix, 18% strand | Q47NR9 |
Ligands and binding sites
- XAG · N-{2-[(2-aminoethyl)sulfanyl]ethyl}-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.85 | 0.85 | 133 | empty |
| 2 | 549 | 0.84 | 0.90 | 81 | empty |
| 3 | 886 | 0.79 | 0.81 | 106 | empty |
| 4 | 212 | 0.60 | 0.81 | 22 | empty |
| 5 | 61 | 0.31 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 462 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7KW0 · Non-ribosomal didomain (stabilised glycine-PCP-C) acceptor bound state · the same entry in another collection · chain A against A, TM-score 1.00
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 Q47NR9
- Elsewhere: RCSB PDB 7KW0 · PDBe 7KW0 · UniProt Q47NR9
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