MolNFT v1 · #46132 · protein
The X-ray crystal structure of the paramecium bursaria chlorella virus arginine decarboxylase
2NV9 · A207R protein, arginine decarboxylase: “The X-ray crystal structure of the paramecium bursaria chlorella virus arginine decarboxylase”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.82). MolNFT v1 #46132 on…
- PDB
- 2NV9
- Type
- protein
- Length
- 2,941 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A207R protein, arginine decarboxylase
- EC
- 4.1.1.19
- UniProt
- Q84527
- Ligands
- PLP
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 371 | 35% helix, 25% strand | Q84527 |
| B | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 372 | 36% helix, 26% strand | Q84527 |
| C | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 367 | 36% helix, 25% strand | Q84527 |
| D | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 363 | 36% helix, 25% strand | Q84527 |
| E | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 370 | 35% helix, 26% strand | Q84527 |
| F | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 369 | 36% helix, 24% strand | Q84527 |
| G | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 362 | 36% helix, 24% strand | Q84527 |
| H | A207R protein, arginine decarboxylase (EC 4.1.1.19) | protein | 367 | 36% helix, 24% strand | Q84527 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
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 | 648 | 0.82 | 0.87 | 66 | empty |
| 2 | 786 | 0.76 | 0.80 | 98 | PLP |
| 3 | 98 | 0.75 | 0.96 | 32 | PLP |
| 4 | 366 | 0.74 | 0.85 | 45 | empty |
| 5 | 326 | 0.73 | 0.85 | 52 | PLP |
Interfaces
15 interfaces between chains.
- E–F · 2588 Ų buried · 38 hydrogen bonds · protein-protein
- G–H · 2569 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2550 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2547 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 696 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2NV9 · The X-ray Crystal Structure of the Paramecium bursaria Chlorella virus arginine… · 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 Q84527
- Elsewhere: RCSB PDB 2NV9 · PDBe 2NV9 · UniProt Q84527
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