Research workbench
The crystal structure of trematomus bernacchii hemoglobin oxidized by ferricyanide
Analyse The crystal structure of trematomus bernacchii hemoglobin oxidized by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1S5Y
- Type
- protein
- Length
- 556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- P80043, P80044
- Ligands
- HEM, ACE
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha chain | protein | 142 | 77% helix, 0% strand | P80043 |
| B, D | Hemoglobin beta chain | protein | 136 | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.78 | 0.80 | 87 | ACE |
| 2 | 199 | 0.74 | 0.89 | 26 | HEM |
| 3 | 222 | 0.73 | 0.88 | 26 | HEM |
| 4 | 210 | 0.73 | 0.88 | 26 | HEM |
| 5 | 245 | 0.70 | 0.85 | 29 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 817 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 817 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 532 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 530 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 1S5Y · The crystal structure of Trematomus bernacchii hemoglobin oxidized by ferricyanide · 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 1S5Y · PDBe 1S5Y · UniProt P80043 · UniProt P80044
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