Research workbench
Xenon bound in hydrophobic channel of hybrid cluster protein from desulfovibrio vulgaris
Analyse Xenon bound in hydrophobic channel of hybrid cluster protein from desulfovibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E9V
- Type
- protein
- Length
- 553 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydroxylamine reductase
- EC
- 1.7.-.-
- UniProt
- P31101
- Ligands
- FSO, SF4, XE
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydroxylamine reductase (EC 1.7.-.-) | protein | 553 | 51% helix, 12% strand | P31101 |
Ligands and binding sites
- FSO · Iron/sulfur/oxygen hybrid cluster · ligand · chains A
- SF4 · Iron/sulfur cluster · ligand · chains A
- XE · Xenon · ion · 13 copies · chains A
- EDO · 1,2-ethanediol · additive · chains A
- ACY · Acetic acid · additive · chains A
- GOL · Glycerol · additive · chains A
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.70 | 0.92 | 34 | XE |
| 2 | 166 | 0.62 | 0.84 | 29 | empty |
| 3 | 58 | 0.60 | 0.91 | 19 | XE |
| 4 | 165 | 0.53 | 0.80 | 33 | empty |
| 5 | 80 | 0.45 | 0.81 | 20 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 1E9V · Xenon bound in hydrophobic channel of hybrid cluster protein from desulfovibrio vulgaris · the same entry in another collection · chain A against A, TM-score 1.00
- P31101 · AlphaFold monomer V2.0 prediction for hydroxylamine reductase (P31101) · a predicted model of the same protein · 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 P31101
- Elsewhere: RCSB PDB 1E9V · PDBe 1E9V · UniProt P31101
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