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The crystal structure of haemoglobin from atlantic cod
Analyse The crystal structure of haemoglobin from atlantic cod in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HIT
- Type
- protein
- Length
- 1,147 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha 2 chain; Hemoglobin beta 4 chain
- UniProt
- B3F9D9, B3F9D7
- Ligands
- HEM, ACE
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemoglobin alpha 2 chain | protein | 142 | 74% helix, 0% strand | B3F9D9 |
| B, D, F | Hemoglobin beta 4 chain | protein | 145 | 77% helix, 0% strand | B3F9D7 |
| H | Hemoglobin beta 4 chain | protein | 144 | 72% helix, 0% strand | B3F9D7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, F, D, E, G, H
- ACE · Acetyl group · ligand · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1157 | 0.84 | 0.85 | 99 | HEM |
| 2 | 835 | 0.81 | 0.84 | 69 | empty |
| 3 | 594 | 0.81 | 0.86 | 60 | empty |
| 4 | 908 | 0.79 | 0.81 | 99 | HEM |
| 5 | 286 | 0.77 | 0.88 | 41 | HEM |
Interfaces
15 interfaces between chains.
- C–D · 929 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 918 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 893 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 866 Ų buried · 7 hydrogen bonds · protein-protein
- E–H · 598 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6HIT · The crystal structure of haemoglobin from Atlantic cod · the same entry in another collection · chain A against A, TM-score 1.00
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 B3F9D9
- Every structure of UniProt B3F9D7
- Elsewhere: RCSB PDB 6HIT · PDBe 6HIT · UniProt B3F9D9 · UniProt B3F9D7
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