MolNFT v1 · #21312 · protein
The crystal structure of trematomus bernacchii hemoglobin oxidized by air
1S5X · Hemoglobin alpha chain: “The crystal structure of trematomus bernacchii hemoglobin oxidized by air”. X-ray diffraction, 2 ligands (HEM, ACE), 4 pockets (best druggability 0.72). MolNFT v1 #21312 on GenesisL1: 3D structure, binding…
- PDB
- 1S5X
- Type
- protein
- Length
- 278 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- P80043, P80044
- Ligands
- HEM, ACE
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin alpha chain | protein | 142 | 77% helix, 0% strand | P80043 |
| B | Hemoglobin beta chain | protein | 136 | 78% helix, 0% strand | P80044 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A
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 | 232 | 0.72 | 0.87 | 27 | HEM |
| 2 | 187 | 0.69 | 0.86 | 27 | HEM |
| 3 | 175 | 0.49 | 0.77 | 28 | empty |
| 4 | 75 | 0.38 | 0.77 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 822 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1S5X · The crystal structure of Trematomus bernacchii hemoglobin oxidized by air · the same entry in another collection · chain A against A, TM-score 1.00
- P80043 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P80043) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P80044 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P80044) · 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 P80043
- Every structure of UniProt P80044
- Elsewhere: RCSB PDB 1S5X · PDBe 1S5X · UniProt P80043 · UniProt P80044
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.