MolNFT v1 · #21918 · protein
Carbonmonoxy hemoglobin from the teleost fish leiostomus xanthurus
1SPG: “Carbonmonoxy hemoglobin from the teleost fish leiostomus xanthurus”. X-ray diffraction, 3 ligands (HEM, ACE, CMO), 4 pockets (best druggability 0.73). MolNFT v1 #21918 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1SPG
- Type
- protein
- Length
- 290 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin
- UniProt
- P56250, P56251
- Ligands
- HEM, ACE, CMO
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin | protein | 143 | 73% helix, 0% strand | P56250 |
| B | Hemoglobin | protein | 147 | 75% helix, 0% strand | P56251 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A
- CMO · Carbon monoxide · ion · 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 | 238 | 0.73 | 0.87 | 26 | HEM, CMO |
| 2 | 232 | 0.72 | 0.87 | 26 | HEM, CMO |
| 3 | 121 | 0.50 | 0.80 | 22 | empty |
| 4 | 69 | 0.37 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 988 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1SPG · Carbonmonoxy hemoglobin from the teleost fish leiostomus xanthurus · the same entry in another collection · chain A against A, TM-score 1.00
- P56251 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P56251) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P56250 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P56250) · a predicted model of the same protein · chain A 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 P56250
- Every structure of UniProt P56251
- Elsewhere: RCSB PDB 1SPG · PDBe 1SPG · UniProt P56250 · UniProt P56251
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