Research workbench
Structure of the nitric oxide complex of reduced shp, an oxygen binding cytochrome C
Analyse Structure of the nitric oxide complex of reduced shp, an oxygen binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DW2
- Type
- protein
- Length
- 336 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C
- UniProt
- P81238
- Ligands
- HEM, NO
- Pockets
- 3 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Cytochrome C | protein | 112 | 46% helix, 4% strand | P81238 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C
- NO · Nitric oxide · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 401 | 0.78 | 0.87 | 63 | HEM, NO |
| 2 | 290 | 0.72 | 0.86 | 36 | HEM, NO |
| 3 | 282 | 0.70 | 0.84 | 34 | HEM, NO |
Interfaces
1 interface between chains.
- B–C · 622 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor, 3 disulfide (heme attachment, disulfide).
Compared structures
- 1DW2 · Structure of the nitric oxide complex of reduced shp, an oxygen binding cytochrome C · the same entry in another collection · chain A against A, TM-score 1.00
- P81238 · AlphaFold monomer V2.0 prediction for cytochrome C-type protein shp (P81238) · 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 P81238
- Elsewhere: RCSB PDB 1DW2 · PDBe 1DW2 · UniProt P81238
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