MolNFT v1 · #72668 · protein
The crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state
3NFE · Hemoglobin subunit alpha-1: “The crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state”. X-ray diffraction, 2 ligands (HEM, ACE), 10 pockets (best druggability 0.80). MolNFT v1 #72668 on GenesisL1: 3D…
- PDB
- 3NFE
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha-1; Hemoglobin subunit beta-1/2
- UniProt
- P45718, P45720
- Ligands
- HEM, ACE
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha-1 | protein | 142 | 75% helix, 0% strand | P45718 |
| B, D | Hemoglobin subunit beta-1/2 | protein | 146 | 74% helix, 0% strand | P45720 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- ACE · Acetyl group · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1192 | 0.80 | 0.82 | 81 | ACE |
| 2 | 216 | 0.74 | 0.88 | 27 | HEM |
| 3 | 215 | 0.72 | 0.87 | 30 | HEM |
| 4 | 213 | 0.72 | 0.87 | 28 | HEM |
| 5 | 221 | 0.66 | 0.83 | 29 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 816 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 795 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 683 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 674 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3NFE · The crystal structure of hemoglobin I from trematomus newnesi in deoxygenated state · the same entry in another collection · chain A against A, TM-score 1.00
- P45720 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-1/2 (P45720) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P45718 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha-1 (P45718) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P45718
- Every structure of UniProt P45720
- Elsewhere: RCSB PDB 3NFE · PDBe 3NFE · UniProt P45718 · UniProt P45720
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.