Research workbench
Doss gafa domain reduced nitric oxide bound crystal structure
Analyse Doss gafa domain reduced nitric oxide bound crystal structure in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YOF
- Type
- protein
- Length
- 281 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Redox sensor histidine kinase response regulator devs
- EC
- 2.7.13.3
- UniProt
- P9WGK2
- Ligands
- HEM, NO
- Pockets
- 3 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Redox sensor histidine kinase response regulator devs (EC 2.7.13.3) | protein | 140 | 39% helix, 24% strand | P9WGK2 |
| B | Redox sensor histidine kinase response regulator devs (EC 2.7.13.3) | protein | 141 | 37% helix, 26% strand | P9WGK2 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- NO · Nitric oxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 313 | 0.80 | 0.90 | 32 | HEM, NO |
| 2 | 323 | 0.78 | 0.88 | 33 | HEM, NO |
| 3 | 106 | 0.41 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 672 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YOF · DosS GAFA Domain Reduced Nitric Oxide Bound Crystal Structure · the same entry in another collection · chain A against A, TM-score 1.00
- P9WGK2 · AlphaFold monomer V2.0 prediction for oxygen sensor histidine kinase response regulator… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P9WGK2
- Elsewhere: RCSB PDB 4YOF · PDBe 4YOF · UniProt P9WGK2
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