Research workbench
Crosslinked alpha(Ni)-beta(Fe-CO) human hemoglobin A in the T quaternary structure at 95 K: Dark
Analyse Crosslinked alpha(Ni)-beta(Fe-CO) human hemoglobin A in the T quaternary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KAH
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.45
- Source
- Homo sapiens
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HNI, HEM, 2FU, CMO
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · resolution 1.45 · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D, F, H | Hemoglobin subunit beta | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HNI · Protoporphyrin IX containing ni(ii) · ligand · 4 copies · chains A, C, E, G
- HEM · Protoporphyrin IX containing Fe · 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 B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.83 | 0.84 | 102 | empty |
| 2 | 1126 | 0.83 | 0.84 | 96 | empty |
| 3 | 509 | 0.79 | 0.85 | 65 | HEM, CMO, HNI |
| 4 | 807 | 0.75 | 0.79 | 60 | HNI |
| 5 | 236 | 0.74 | 0.88 | 29 | HEM, CMO |
Interfaces
13 interfaces between chains.
- C–D · 933 Ų buried · 10 hydrogen bonds · protein-protein
- G–H · 880 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 848 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 700 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6KAH · Crosslinked ALPHA(NI)-BETA(FE-co) human hemoglobin a in the T quaternary structure at 95… · the same entry in another collection · chain H against H, TM-score 1.00
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain G 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 P69905
- Every structure of UniProt P68871
- Elsewhere: RCSB PDB 6KAH · PDBe 6KAH · UniProt P69905 · UniProt P68871
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