MolNFT v1 · #136737 · protein
Crystal structure of pseudomonas brassicacearum lignostilbene dioxygenase
5V2D: “Crystal structure of pseudomonas brassicacearum lignostilbene dioxygenase”. X-ray diffraction, 1 ligand (FE), 20 pockets (best druggability 0.79). MolNFT v1 #136737 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V2D
- Type
- protein
- Length
- 1,931 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dioxygenase
- UniProt
- W8QAY8
- Ligands
- FE
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dioxygenase | protein | 488 | 9% helix, 38% strand | W8QAY8 |
| B | Dioxygenase | protein | 483 | 8% helix, 39% strand | W8QAY8 |
| C, D | Dioxygenase | protein | 480 | 8% helix, 38% strand | W8QAY8 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 497 | 0.79 | 0.85 | 56 | empty |
| 2 | 480 | 0.78 | 0.85 | 62 | empty |
| 3 | 526 | 0.77 | 0.84 | 54 | empty |
| 4 | 511 | 0.77 | 0.84 | 61 | empty |
| 5 | 314 | 0.75 | 0.87 | 47 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1493 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5V2D · Crystal structure of Pseudomonas brassicacearum lignostilbene dioxygenase · 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 W8QAY8
- Elsewhere: RCSB PDB 5V2D · PDBe 5V2D · UniProt W8QAY8
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