Research workbench
Crystal structure of bluefin tuna hemoglobin deoxy form at PH7.5
Analyse Crystal structure of bluefin tuna hemoglobin deoxy form at PH7.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1V4W
- Type
- protein
- Length
- 578 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- Q8AYM0, Q8AYM1
- Ligands
- HEM, ACE
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha chain | protein | 143 | 76% helix, 0% strand | Q8AYM0 |
| B, D | Hemoglobin beta chain | protein | 146 | 77% helix, 0% strand | Q8AYM1 |
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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.81 | 0.83 | 73 | empty |
| 2 | 267 | 0.76 | 0.88 | 31 | HEM |
| 3 | 262 | 0.75 | 0.87 | 31 | HEM |
| 4 | 253 | 0.73 | 0.87 | 27 | HEM |
| 5 | 252 | 0.72 | 0.86 | 30 | HEM |
Interfaces
5 interfaces between chains.
- A–B · 893 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 890 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 709 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 684 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 568 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1V4W · Crystal structure of bluefin tuna hemoglobin deoxy form at pH7.5 · 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 Q8AYM0
- Every structure of UniProt Q8AYM1
- Elsewhere: RCSB PDB 1V4W · PDBe 1V4W · UniProt Q8AYM0 · UniProt Q8AYM1
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