MolNFT v1 · #137107 · protein
Crystal structure of persulfide dioxygenase rhodanese fusion protein with rhodanese domain inactivating mutation (C314S) from burkholderia phytofirmans in complex with glutathione
5VE5 · Bpprf: “Crystal structure of persulfide dioxygenase rhodanese fusion protein with rhodanese domain inactivating…”. X-ray diffraction, 3 ligands (GSH, FE, CL), 13 pockets (best druggability 0.68). MolNFT v1 #137107 on GenesisL1: 3D…
- 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
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