Research workbench
Crystal structure of the cathodic hemoglobin isolated from the antarctic fish trematomus newnesi
Analyse Crystal structure of the cathodic hemoglobin isolated from the antarctic fish… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AA1
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha-1 chain; Hemoglobin beta-C chain
- UniProt
- P45718, P45721
- Ligands
- HEM, ACE
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha-1 chain | protein | 142 | 76% helix, 0% strand | P45718 |
| B, D | Hemoglobin beta-C chain | protein | 146 | 79% helix, 0% strand | P45721 |
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
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 909 | 0.82 | 0.84 | 75 | ACE |
| 2 | 216 | 0.74 | 0.89 | 33 | HEM |
| 3 | 246 | 0.70 | 0.85 | 31 | HEM |
| 4 | 226 | 0.70 | 0.86 | 28 | HEM |
| 5 | 206 | 0.70 | 0.86 | 28 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 817 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 782 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 704 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 702 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 488 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2AA1 · Crystal structure of the cathodic hemoglobin isolated from the Antarctic fish Trematomus… · the same entry in another collection · chain A against A, TM-score 1.00
- 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
- P45721 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-C (P45721) · 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 P45718
- Every structure of UniProt P45721
- Elsewhere: RCSB PDB 2AA1 · PDBe 2AA1 · UniProt P45718 · UniProt P45721
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