Research workbench
Crystal structure of cytoglobin: the fourth globin type discovered in man displays heme hexa-coordination
Analyse Crystal structure of cytoglobin: the fourth globin type discovered in man… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1URV
- Type
- protein
- Length
- 308 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytoglobin
- UniProt
- Q8WWM9
- Ligands
- HEM, FC6
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytoglobin | protein | 154 | 79% helix, 0% strand | Q8WWM9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- FC6 · Hexacyanoferrate(3-) · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.73 | 0.87 | 34 | HEM |
| 2 | 532 | 0.73 | 0.81 | 68 | HEM, FC6 |
| 3 | 347 | 0.57 | 0.76 | 40 | FC6 |
Interfaces
1 interface between chains.
- A–B · 644 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1URV · Crystal structure of cytoglobin: the fourth globin type discovered in man displays heme… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8WWM9 · AlphaFold monomer V2.0 prediction for cytoglobin (Q8WWM9) · a predicted model of the same protein · chain A 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 Q8WWM9
- Elsewhere: RCSB PDB 1URV · PDBe 1URV · UniProt Q8WWM9
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