MolNFT v1 · #82577 · protein
The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms
3VRF · Hemoglobin subunit alpha: “The crystal structure of hemoglobin from woolly mammoth in the carbonmonoxy forms”. X-ray diffraction, 2 ligands (HEM, CMO), 4 pockets (best druggability 0.73). MolNFT v1 #82577 on GenesisL1: 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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