Research workbench
Crystal structure of persulfide dioxygenase rhodanese fusion protein with rhodanese domain inactivating mutation (C314S) from burkholderia phytofirmans in complex with glutathione
Analyse Crystal structure of persulfide dioxygenase rhodanese fusion protein with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VE5
- Type
- protein
- Length
- 1,046 residues
- Chains
- 3
- 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
- GSH, FE, CL
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bpprf (EC 1.13.11.18, 2.8.1.1) | protein | 350 | 29% helix, 25% strand | B2TEQ2 |
| B | Bpprf (EC 1.13.11.18, 2.8.1.1) | protein | 349 | 28% helix, 26% strand | B2TEQ2 |
| C | Bpprf (EC 1.13.11.18, 2.8.1.1) | protein | 347 | 29% helix, 25% strand | B2TEQ2 |
Ligands and binding sites
- GSH · Glutathione · ligand · 3 copies · chains A, B, C
- FE · Fe (III) ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- IMD · Imidazole · additive · 2 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.68 | 0.77 | 56 | empty |
| 2 | 384 | 0.67 | 0.80 | 41 | GSH |
| 3 | 509 | 0.65 | 0.77 | 60 | GSH |
| 4 | 271 | 0.60 | 0.79 | 46 | empty |
| 5 | 200 | 0.59 | 0.81 | 32 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2051 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 245 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5VE5 · Crystal structure of persulfide dioxygenase rhodanese fusion protein with rhodanese… · 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 B2TEQ2
- Elsewhere: RCSB PDB 5VE5 · PDBe 5VE5 · UniProt B2TEQ2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.