Research workbench
The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms
Analyse The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VRF
- Type
- protein
- Length
- 287 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit BETA/DELTA hybrid
- UniProt
- D3U1H8, D3U1H9
- Ligands
- HEM, CMO
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 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 | D3U1H8 |
| B | Hemoglobin subunit BETA/DELTA hybrid | protein | 146 | 81% helix, 0% strand | D3U1H9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CMO · Carbon monoxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 232 | 0.73 | 0.87 | 27 | HEM, CMO |
| 2 | 198 | 0.71 | 0.87 | 26 | HEM, CMO |
| 3 | 180 | 0.52 | 0.78 | 29 | empty |
| 4 | 59 | 0.34 | 0.77 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 954 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3VRF · The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms · the same entry in another collection · chain A against A, TM-score 1.00
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 D3U1H8
- Every structure of UniProt D3U1H9
- Elsewhere: RCSB PDB 3VRF · PDBe 3VRF · UniProt D3U1H8 · UniProt D3U1H9
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