Research workbench
Horse methemoglobin low salt, pH 7.0 (88% relative humidity)
Analyse Horse methemoglobin low salt, pH 7.0 (88% relative humidity) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y8K
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chains; Hemoglobin beta chain
- UniProt
- P01958, P02062
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin alpha chains | protein | 141 | 77% helix, 0% strand | P01958 |
| B, D | Hemoglobin beta chain | protein | 146 | 81% helix, 0% strand | P02062 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.84 | 0.89 | 75 | empty |
| 2 | 260 | 0.74 | 0.87 | 30 | HEM |
| 3 | 275 | 0.74 | 0.86 | 31 | HEM |
| 4 | 195 | 0.70 | 0.86 | 22 | HEM |
| 5 | 194 | 0.69 | 0.86 | 24 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 925 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 906 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 550 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 352 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1Y8K · Horse methemoglobin low salt, PH 7.0 (88% relative humidity) · the same entry in another collection · chain A against A, TM-score 1.00
- P02062 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P02062) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P01958 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P01958) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P01958
- Every structure of UniProt P02062
- Elsewhere: RCSB PDB 1Y8K · PDBe 1Y8K · UniProt P01958 · UniProt P02062
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