MolNFT v1 · #169411 · protein
Structure of acnpv poxin in post-reactive state with GP[2'-5']AP[3']
6XB3: “Structure of acnpv poxin in post-reactive state with GP[2'-5']AP[3']”. X-ray diffraction, 1 ligand (9BG), 20 pockets (best druggability 0.82). MolNFT v1 #169411 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XB3
- Type
- protein
- Length
- 3,636 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Poxin
- EC
- 3.1.-.-
- UniProt
- P08358
- Ligands
- 9BG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 15 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Poxin (EC 3.1.-.-) | protein | 234 | 9% helix, 50% strand | P08358 |
| B, I | Poxin (EC 3.1.-.-) | protein | 229 | 9% helix, 50% strand | P08358 |
| C | Poxin (EC 3.1.-.-) | protein | 226 | 9% helix, 50% strand | P08358 |
| D | Poxin (EC 3.1.-.-) | protein | 225 | 8% helix, 52% strand | P08358 |
| E | Poxin (EC 3.1.-.-) | protein | 231 | 9% helix, 52% strand | P08358 |
| F | Poxin (EC 3.1.-.-) | protein | 220 | 9% helix, 52% strand | P08358 |
| G | Poxin (EC 3.1.-.-) | protein | 226 | 8% helix, 51% strand | P08358 |
| H | Poxin (EC 3.1.-.-) | protein | 232 | 9% helix, 50% strand | P08358 |
| J | Poxin (EC 3.1.-.-) | protein | 231 | 9% helix, 50% strand | P08358 |
| K | Poxin (EC 3.1.-.-) | protein | 223 | 9% helix, 51% strand | P08358 |
| L | Poxin (EC 3.1.-.-) | protein | 225 | 8% helix, 52% strand | P08358 |
| M | Poxin (EC 3.1.-.-) | protein | 226 | 9% helix, 52% strand | P08358 |
| N | Poxin (EC 3.1.-.-) | protein | 224 | 9% helix, 50% strand | P08358 |
| O | Poxin (EC 3.1.-.-) | protein | 227 | 8% helix, 51% strand | P08358 |
| P | Poxin (EC 3.1.-.-) | protein | 228 | 9% helix, 52% strand | P08358 |
Ligands and binding sites
- 9BG · 2',5'-GpAp · ligand · 16 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.82 | 0.91 | 53 | empty |
| 2 | 441 | 0.82 | 0.89 | 59 | empty |
| 3 | 422 | 0.81 | 0.89 | 59 | empty |
| 4 | 428 | 0.81 | 0.89 | 60 | empty |
| 5 | 460 | 0.81 | 0.88 | 67 | empty |
Interfaces
24 interfaces between chains.
- G–H · 1364 Ų buried · 28 hydrogen bonds · protein-protein
- I–J · 1353 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1324 Ų buried · 27 hydrogen bonds · protein-protein
- O–P · 1309 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1307 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6XB3 · Structure of AcNPV poxin in post-reactive state with Gp[2'-5']Ap[3'] · the same entry in another collection · chain L against L, 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 P08358
- Elsewhere: RCSB PDB 6XB3 · PDBe 6XB3 · UniProt P08358
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