MolNFT v1 · #188816 · protein
Crystal structure of liganded hb with the 5-hmf analog, MMA509
7UF6 · Hemoglobin subunit alpha: “Crystal structure of liganded hb with the 5-hmf analog, MMA509”. X-ray diffraction, 3 ligands (HEM, N1X, CMO), 5 pockets (best druggability 0.85). MolNFT v1 #188816 on GenesisL1: 3D structure, binding…
- PDB
- 7UF6
- Type
- protein
- Length
- 574 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, N1X, CMO
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin subunit alpha | protein | 141 | 75% helix, 0% strand | P69905 |
| B, D | Hemoglobin subunit beta | protein | 146 | 78% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- N1X · (2S)-2-(5-methylfuran-2-yl)oxane · ligand · 2 copies · chains A, C
- CMO · Carbon monoxide · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.85 | 0.86 | 123 | N1X |
| 2 | 244 | 0.75 | 0.88 | 28 | HEM, CMO |
| 3 | 212 | 0.74 | 0.88 | 26 | HEM, CMO |
| 4 | 207 | 0.71 | 0.87 | 24 | HEM, CMO |
| 5 | 185 | 0.69 | 0.86 | 24 | HEM, CMO |
Interfaces
6 interfaces between chains.
- C–D · 926 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 895 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 462 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 411 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 385 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 7UF6 · Crystal structure of liganded Hb with the 5-HMF analog, MMA509 · the same entry in another collection · chain D against D, TM-score 1.00
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P69905 · AlphaFold monomer V2.0 prediction for hemoglobin subunit alpha (P69905) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 7UF6 · PDBe 7UF6 · UniProt P69905 · UniProt P68871
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.