Research workbench
Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion protein from burkholderia phytofirmans
Analyse Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VE3
- Type
- protein
- Length
- 696 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bpprf
- EC
- 1.13.11.18, 2.8.1.1
- UniProt
- B2TEQ2
- Ligands
- FE
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | Bpprf (EC 1.13.11.18, 2.8.1.1) | protein | 348 | 29% helix, 26% strand | B2TEQ2 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains B, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 514 | 0.68 | 0.78 | 63 | FE |
| 2 | 585 | 0.67 | 0.77 | 55 | empty |
| 3 | 409 | 0.64 | 0.78 | 41 | empty |
| 4 | 212 | 0.58 | 0.80 | 33 | empty |
| 5 | 176 | 0.57 | 0.81 | 31 | empty |
Interfaces
1 interface between chains.
- B–A · 2025 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5VE3 · Crystal structure of wild-type persulfide dioxygenase-rhodanese fusion protein from… · 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 B2TEQ2
- Elsewhere: RCSB PDB 5VE3 · PDBe 5VE3 · UniProt B2TEQ2
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