Research workbench
Crystal structure of rat methemoglobin in R2 state
Analyse Crystal structure of rat methemoglobin in R2 state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3HF4
- Type
- protein
- Length
- 573 residues
- Chains
- 4
- 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
- 6 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Hemoglobin subunit alpha-1/2 | protein | 141 | 79% helix, 0% strand | P01946 |
| B | Hemoglobin subunit beta-1 | protein | 145 | 80% helix, 0% strand | P02091 |
| F | Hemoglobin subunit beta-1 | protein | 146 | 79% helix, 0% strand | P02091 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.86 | 0.89 | 108 | empty |
| 2 | 277 | 0.74 | 0.87 | 29 | HEM |
| 3 | 262 | 0.74 | 0.87 | 30 | HEM |
| 4 | 258 | 0.73 | 0.86 | 25 | HEM |
| 5 | 195 | 0.72 | 0.88 | 24 | HEM |
Interfaces
6 interfaces between chains.
- E–F · 943 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 911 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 498 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 468 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 382 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3HF4 · Crystal structure of rat methemoglobin in R2 state · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- 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 0.97
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 3HF4 · PDBe 3HF4 · UniProt P01946 · UniProt P02091
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