Research workbench
Cysteine persulfide intermediate of nifs from helicobacter pylori
Analyse Cysteine persulfide intermediate of nifs from helicobacter pylori in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WT6
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cysteine desulfurase iscs
- EC
- 2.8.1.7
- UniProt
- O25008
- Ligands
- PDA, CL
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cysteine desulfurase iscs (EC 2.8.1.7) | protein | 366 | 40% helix, 17% strand | O25008 |
Ligands and binding sites
- PDA · 2-[(3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl)-amino]-propionic acid · ligand · chains A
- CL · Chloride ion · ion · chains A
- IPA · Isopropyl alcohol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.45 | 0.82 | 18 | PDA |
| 2 | 130 | 0.44 | 0.77 | 23 | empty |
| 3 | 52 | 0.27 | 0.74 | 16 | IPA |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5WT6 · Cysteine persulfide intermediate of NifS from Helicobacter pylori · the same entry in another collection · chain A against A, TM-score 1.00
- O25008 · AlphaFold monomer V2.0 prediction for cysteine desulfurase iscs (O25008) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 O25008
- Elsewhere: RCSB PDB 5WT6 · PDBe 5WT6 · UniProt O25008
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