Research workbench
Joint X-ray/neutron structure of equine cyanomet hemoglobin in R state
Analyse Joint X-ray/neutron structure of equine cyanomet hemoglobin in R state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5C6E
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction, neutron diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7,2
- Source
- Equus caballus
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P01958, P02062
- Ligands
- HEM, CYN
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction, neutron diffraction · resolution 1.7,2 · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P01958 |
| B | Hemoglobin subunit beta | protein | 146 | 81% helix, 0% strand | P02062 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.72 | 0.86 | 28 | HEM, CYN |
| 2 | 214 | 0.70 | 0.86 | 24 | HEM, CYN |
| 3 | 198 | 0.54 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 876 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5C6E · Joint X-RAY/NEUTRON structure of equine cyanomet hemoglobin in R state · the same entry in another collection · chain A against A, TM-score 1.00
- P02062 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02062) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01958 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01958) · 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 P01958
- Every structure of UniProt P02062
- Elsewhere: RCSB PDB 5C6E · PDBe 5C6E · UniProt P01958 · UniProt P02062
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