MolNFT v1 · #154411 · protein
Crosslinked ALPHA(FE-co)-BETA(NI) human hemoglobin a in the T quaternary structure at 95 K: dark
6KA9 · Hemoglobin subunit alpha: “Crosslinked ALPHA(FE-co)-BETA(NI) human hemoglobin a in the T quaternary structure at 95 K: dark”. X-ray diffraction, 4 ligands (HEM, HNI, 2FU), 18 pockets (best druggability 0.82). MolNFT v1 #154411 on…
- PDB
- 6KA9
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, HNI, 2FU, CMO
- Pockets
- 18 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemoglobin subunit alpha | protein | 141 | 75% helix, 0% strand | P69905 |
| B, D, F, H | Hemoglobin subunit beta | 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
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1069 | 0.82 | 0.83 | 103 | empty |
| 2 | 887 | 0.81 | 0.83 | 93 | empty |
| 3 | 750 | 0.75 | 0.79 | 59 | HEM, CMO |
| 4 | 232 | 0.74 | 0.88 | 30 | HEM, CMO |
| 5 | 216 | 0.73 | 0.88 | 32 | HNI |
Interfaces
13 interfaces between chains.
- G–H · 849 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 846 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 841 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 840 Ų buried · 10 hydrogen bonds · protein-protein
- E–H · 724 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6KA9 · Crosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T quaternary structure at 95… · 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 6KA9 · PDBe 6KA9 · UniProt P69905 · UniProt P68871
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