MolNFT v1 · #46903 · protein
The crystal structure of ferric cyanide bound barley hexacoordinate hemoglobin.
2OIF · Non-legume hemoglobin: “The crystal structure of ferric cyanide bound barley hexacoordinate hemoglobin.”. X-ray diffraction, 2 ligands (HEM, CYN), 17 pockets (best druggability 0.81). MolNFT v1 #46903 on GenesisL1: 3D structure…
- PDB
- 2OIF
- Type
- protein
- Length
- 1,219 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-legume hemoglobin
- UniProt
- Q42831
- Ligands
- HEM, CYN
- Pockets
- 17 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-legume hemoglobin | protein | 153 | 76% helix, 0% strand | Q42831 |
| B | Non-legume hemoglobin | protein | 151 | 77% helix, 0% strand | Q42831 |
| C, D, F, H | Non-legume hemoglobin | protein | 152 | 76% helix, 0% strand | Q42831 |
| E | Non-legume hemoglobin | protein | 153 | 76% helix, 0% strand | Q42831 |
| G | Non-legume hemoglobin | protein | 154 | 75% helix, 0% strand | Q42831 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CYN · Cyanide ion · ion · 8 copies · chains A, B, C, D, E, F, G, H
- PGO · S-1,2-propanediol · additive · 13 copies · chains A, F, B, C, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.81 | 0.85 | 72 | CYN, HEM, PGO |
| 2 | 704 | 0.81 | 0.85 | 71 | CYN, HEM, PGO |
| 3 | 690 | 0.80 | 0.84 | 71 | CYN, HEM, PGO |
| 4 | 677 | 0.80 | 0.84 | 73 | CYN, HEM, PGO |
| 5 | 120 | 0.50 | 0.80 | 31 | empty |
Interfaces
10 interfaces between chains.
- G–H · 492 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 491 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 490 Ų buried · 11 hydrogen bonds · protein-protein
- A–F · 488 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 417 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2OIF · The crystal structure of ferric cyanide bound barley hexacoordinate hemoglobin. · the same entry in another collection · chain H against H, TM-score 1.00
- Q42831 · AlphaFold monomer V2.0 prediction for non-symbiotic hemoglobin (Q42831) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q42831
- Elsewhere: RCSB PDB 2OIF · PDBe 2OIF · UniProt Q42831
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