MolNFT v1 · #169412 · protein
Structure of prgv poxin in post-reactive state with GP[2'-5']AP[3']
6XB4: “Structure of prgv poxin in post-reactive state with GP[2'-5']AP[3']”. X-ray diffraction, 1 ligand (9BG), 13 pockets (best druggability 0.79). MolNFT v1 #169412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XB4
- Type
- protein
- Length
- 765 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poxin
- UniProt
- V9XTR0
- Ligands
- 9BG
- Pockets
- 13 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poxin | protein | 199 | 10% helix, 47% strand | V9XTR0 |
| B | Poxin | protein | 191 | 9% helix, 48% strand | V9XTR0 |
| C | Poxin | protein | 189 | 10% helix, 48% strand | V9XTR0 |
| D | Poxin | protein | 186 | 4% helix, 50% strand | V9XTR0 |
Ligands and binding sites
- 9BG · 2',5'-GpAp · ligand · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 997 | 0.79 | 0.81 | 86 | 9BG |
| 2 | 811 | 0.79 | 0.82 | 72 | empty |
| 3 | 444 | 0.71 | 0.81 | 39 | 9BG |
| 4 | 403 | 0.70 | 0.81 | 31 | 9BG |
| 5 | 286 | 0.62 | 0.80 | 34 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1229 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1160 Ų buried · 31 hydrogen bonds · protein-protein
- A–D · 400 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 280 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 183 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6XB4 · Structure of PrGV poxin in post-reactive state with Gp[2'-5']Ap[3'] · 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 V9XTR0
- Elsewhere: RCSB PDB 6XB4 · PDBe 6XB4 · UniProt V9XTR0
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