Research workbench
Human hemoglobin in complex with nitrosoamphetamine
Analyse Human hemoglobin in complex with nitrosoamphetamine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JJQ
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM, K7M
- Pockets
- 13 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin subunit alpha | protein | 140 | 78% helix, 0% strand | P69905 |
| B | Hemoglobin subunit beta | protein | 145 | 70% helix, 0% strand | P68871 |
| C | Hemoglobin subunit alpha | protein | 139 | 79% helix, 0% strand | P69905 |
| D | Hemoglobin subunit beta | protein | 144 | 73% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- K7M · (2R)-N-hydroxy-1-phenylpropan-2-amine · ligand · 3 copies · chains B, C, D
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.88 | 0.90 | 86 | empty |
| 2 | 451 | 0.81 | 0.88 | 46 | HEM, K7M |
| 3 | 420 | 0.80 | 0.87 | 36 | HEM, K7M |
| 4 | 117 | 0.77 | 0.95 | 18 | K7M |
| 5 | 120 | 0.77 | 0.95 | 22 | GOL |
Interfaces
6 interfaces between chains.
- C–D · 937 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 884 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 529 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 486 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 197 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7JJQ · Human Hemoglobin in Complex with Nitrosoamphetamine · the same entry in another collection · chain D against D, TM-score 1.00
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 7JJQ · PDBe 7JJQ · UniProt P69905 · UniProt P68871
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