MolNFT v1 · #8874 · protein
Macromolecular structure refinement by restrained least-squares and interactive graphics as applied to sickling deer type III hemoglobin
1HDS · Hemoglobin S (deoxy) (alpha chain): “Macromolecular structure refinement by restrained least-squares and interactive graphics as applied to…”. X-ray diffraction, 1 ligand (HEM), 8 pockets (best druggability 0.87). MolNFT v1 #8874 on…
- PDB
- 1HDS
- Type
- protein
- Length
- 572 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin S (deoxy) (alpha chain); Hemoglobin S (deoxy) (beta chain)
- UniProt
- P01972, P02074
- Ligands
- HEM
- Pockets
- 8 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 58% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin S (deoxy) (alpha chain) | protein | 141 | 60% helix, 1% strand | P01972 |
| B, D | Hemoglobin S (deoxy) (beta chain) | protein | 145 | 57% helix, 0% strand | P02074 |
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
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1181 | 0.87 | 0.88 | 111 | empty |
| 2 | 346 | 0.78 | 0.88 | 33 | HEM |
| 3 | 281 | 0.73 | 0.86 | 30 | HEM |
| 4 | 214 | 0.72 | 0.87 | 32 | HEM |
| 5 | 210 | 0.71 | 0.87 | 31 | HEM |
Interfaces
6 interfaces between chains.
- A–B · 857 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 836 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 548 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 454 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 400 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (heme attachment).
Compared structures
- 1HDS · Macromolecular structure refinement by restrained least-squares and interactive graphics… · the same entry in another collection · chain A against A, TM-score 1.00
- P02074 · AlphaFold monomer V2.0 prediction for hemoglobin subunit beta-3 (P02074) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P01972
- Every structure of UniProt P02074
- Elsewhere: RCSB PDB 1HDS · PDBe 1HDS · UniProt P01972 · UniProt P02074
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