Research workbench
The crystal structure of hemoglobin from woolly mammoth in the deoxy form
Analyse The crystal structure of hemoglobin from woolly mammoth in the deoxy form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VRE
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- 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
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | D3U1H8 |
| B, D | Hemoglobin subunit BETA/DELTA hybrid | protein | 146 | 79% helix, 0% strand | D3U1H9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1162 | 0.83 | 0.84 | 90 | empty |
| 2 | 247 | 0.74 | 0.87 | 30 | HEM |
| 3 | 218 | 0.73 | 0.88 | 29 | HEM |
| 4 | 215 | 0.73 | 0.87 | 27 | HEM |
| 5 | 249 | 0.71 | 0.86 | 30 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 947 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 910 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 716 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 714 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 309 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3VRE · The crystal structure of hemoglobin from woolly mammoth in the deoxy form · 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 3VRE · PDBe 3VRE · UniProt D3U1H8 · UniProt D3U1H9
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