Research workbench
Crystal structure of deoxy hemoglobin from trematomus bernacchii at pH 8.4
Analyse Crystal structure of deoxy hemoglobin from trematomus bernacchii at pH 8.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2H8D
- Type
- protein
- Length
- 576 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha subunit; Hemoglobin beta subunit
- UniProt
- P80043, P80044
- Ligands
- HEM, ACE, K
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha subunit | protein | 142 | 76% helix, 0% strand | P80043 |
| B, D | Hemoglobin beta subunit | protein | 146 | 77% helix, 0% strand | P80044 |
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
- K · Potassium ion · metal · 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 | 947 | 0.83 | 0.84 | 73 | ACE |
| 2 | 215 | 0.73 | 0.88 | 26 | HEM |
| 3 | 261 | 0.71 | 0.85 | 32 | HEM |
| 4 | 210 | 0.71 | 0.87 | 28 | HEM |
| 5 | 251 | 0.68 | 0.84 | 30 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 853 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 815 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 726 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 673 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 504 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2H8D · Crystal structure of deoxy hemoglobin from Trematomus bernacchii at pH 8.4 · the same entry in another collection · chain A against A, TM-score 1.00
- P80044 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P80044) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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
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 2H8D · PDBe 2H8D · UniProt P80043 · UniProt P80044
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