MolNFT v1 · #189379 · protein
3.6 a structure of the human hemoglobin
7VDE · Hemoglobin subunit alpha: “3.6 a structure of the human hemoglobin”. Electron microscopy, 1 ligand (HEM), 7 pockets (best druggability 0.83). MolNFT v1 #189379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VDE
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin subunit alpha; Hemoglobin subunit beta
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 7 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 77% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 75% helix, 0% strand | P68871 |
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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.83 | 0.84 | 116 | empty |
| 2 | 360 | 0.75 | 0.85 | 30 | HEM |
| 3 | 338 | 0.74 | 0.85 | 27 | HEM |
| 4 | 306 | 0.72 | 0.84 | 25 | HEM |
| 5 | 272 | 0.71 | 0.85 | 26 | HEM |
Interfaces
6 interfaces between chains.
- C–D · 850 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 845 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 382 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 381 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 199 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7VDE · 3.6 A structure of the human hemoglobin · 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 0.97
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 7VDE · PDBe 7VDE · UniProt P69905 · UniProt P68871
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