Research workbench
Direct observation of photolysis-induced tertiary structural changes in human hemoglobin; crystal structure of ALPHA(FE)-BETA(NI) hemoglobin (laser photolysed)
Analyse Direct observation of photolysis-induced tertiary structural changes in human… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J3Y
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- P69905, P68871
- Ligands
- HEM, HNI, 2FU, CMO
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemoglobin alpha chain | protein | 141 | 76% helix, 0% strand | P69905 |
| B, D, F, H | Hemoglobin beta chain | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, E, G
- HNI · Protoporphyrin IX containing ni(ii) · ligand · 4 copies · chains B, D, F, H
- 2FU · But-2-enedial · ligand · 2 copies · chains B, D, F, H
- CMO · Carbon monoxide · ion · 4 copies · chains A, C, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.79 | 0.83 | 72 | empty |
| 2 | 473 | 0.78 | 0.86 | 66 | empty |
| 3 | 233 | 0.75 | 0.88 | 29 | HEM, CMO |
| 4 | 817 | 0.75 | 0.79 | 65 | HEM, CMO |
| 5 | 220 | 0.74 | 0.88 | 31 | HNI |
Interfaces
13 interfaces between chains.
- C–D · 887 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 862 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 862 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 851 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 730 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1J3Y · Direct observation of photolysis-induced tertiary structural changes in human hemoglobin… · 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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 1J3Y · PDBe 1J3Y · UniProt P69905 · UniProt P68871
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