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Haemoglobin of the antarctic fish pagothenia bernacchii: amino acid sequence, oxygen equilibria and crystal structure of its carbonmonoxy derivative
Analyse Haemoglobin of the antarctic fish pagothenia bernacchii: amino acid sequence… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PBX
- Type
- protein
- Length
- 288 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin (carbonmonoxy) (alpha chain); Hemoglobin (carbonmonoxy) (beta chain)
- UniProt
- P80043, P80044
- Ligands
- HEM, ACE, CMO
- 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 (carbonmonoxy) (alpha chain) | protein | 142 | 77% helix, 0% strand | P80043 |
| B | Hemoglobin (carbonmonoxy) (beta chain) | protein | 146 | 79% 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
- 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.72 | 0.87 | 26 | HEM, CMO |
| 2 | 222 | 0.71 | 0.86 | 29 | HEM, CMO |
| 3 | 213 | 0.53 | 0.77 | 34 | empty |
| 4 | 71 | 0.37 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 862 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1PBX · Haemoglobin of the antarctic fish pagothenia bernacchii: amino acid sequence, oxygen… · 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 1PBX · PDBe 1PBX · UniProt P80043 · UniProt P80044
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