MolNFT v2 · #13568 · protein
Deoxy hemoglobin (90% relative humidity)
1LFL · Hemoglobin alpha chain: “Deoxy hemoglobin (90% relative humidity)”. X-ray diffraction at 2.7, 1 ligand (HEM), 18 pockets (best druggability 0.81). MolNFT v2 #13568 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1LFL
- Type
- protein
- Length
- 1,148 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Homo sapiens
- Molecule
- Hemoglobin alpha chain; Hemoglobin beta chain
- UniProt
- P69905, P68871
- Ligands
- HEM
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.7 · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, P, R | Hemoglobin alpha chain | protein | 141 | 75% helix, 0% strand | P69905 |
| B, D, Q, S | Hemoglobin beta chain | protein | 146 | 77% helix, 0% strand | P68871 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, P, Q, R, S
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.81 | 0.83 | 78 | empty |
| 2 | 876 | 0.81 | 0.83 | 87 | empty |
| 3 | 269 | 0.73 | 0.86 | 29 | HEM |
| 4 | 251 | 0.73 | 0.87 | 29 | HEM |
| 5 | 228 | 0.73 | 0.87 | 28 | HEM |
Interfaces
10 interfaces between chains.
- P–Q · 882 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 863 Ų buried · 12 hydrogen bonds · protein-protein
- R–S · 828 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 827 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 720 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1LFL · Deoxy hemoglobin (90% relative humidity) · the same entry in another collection · chain S against S, 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 1.00
- P68871 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta (P68871) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 1LFL · PDBe 1LFL · UniProt P69905 · UniProt P68871
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