Research workbench
The crystal structure determination of rat (rattus norvegicus) hemoglobin
Analyse The crystal structure determination of rat (rattus norvegicus) hemoglobin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DHT
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-1/2; Hemoglobin subunit beta-1
- UniProt
- P01946, P02091
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha-1/2 | protein | 139 | 75% helix, 0% strand | P01946 |
| B | Hemoglobin subunit beta-1 | protein | 145 | 70% helix, 0% strand | P02091 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.75 | 0.88 | 26 | HEM |
| 2 | 254 | 0.72 | 0.86 | 26 | HEM |
| 3 | 107 | 0.49 | 0.81 | 21 | empty |
| 4 | 62 | 0.34 | 0.77 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 970 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3DHT · The Crystal Structure Determination of Rat (rattus norvegicus) Hemoglobin · the same entry in another collection · chain B against B, TM-score 1.00
- P01946 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-1/2 (P01946) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P02091 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-1 (P02091) · a predicted model of the same protein · chain B 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 P01946
- Every structure of UniProt P02091
- Elsewhere: RCSB PDB 3DHT · PDBe 3DHT · UniProt P01946 · UniProt P02091
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