MolNFT v1 · #186668 · protein
Crystal structure of potato leafroll virus (plrv) coat protein
7RLM: “Crystal structure of potato leafroll virus (plrv) coat protein”. X-ray diffraction, 1 ligand (BR), 7 pockets (best druggability 0.65). MolNFT v1 #186668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RLM
- Type
- protein
- Length
- 848 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein
- UniProt
- Q76QV9
- Ligands
- BR
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, D, E, F | Coat protein | protein | 141 | 9% helix, 53% strand | Q76QV9 |
| A, C | Coat protein | protein | 142 | 9% helix, 53% strand | Q76QV9 |
Ligands and binding sites
- BR · Bromide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 452 | 0.65 | 0.78 | 73 | empty |
| 2 | 600 | 0.65 | 0.76 | 74 | empty |
| 3 | 484 | 0.61 | 0.75 | 45 | empty |
| 4 | 167 | 0.45 | 0.75 | 34 | empty |
| 5 | 51 | 0.33 | 0.78 | 13 | empty |
Interfaces
8 interfaces between chains.
- D–E · 477 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 465 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 463 Ų buried · 6 hydrogen bonds · protein-protein
- B–A · 457 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 268 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7RLM · Crystal Structure of Potato Leafroll Virus (PLRV) Coat Protein · the same entry in another collection · chain B against B, 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 Q76QV9
- Elsewhere: RCSB PDB 7RLM · PDBe 7RLM · UniProt Q76QV9
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