Research workbench
Analysis of the crystal structure, molecular modeling and infrared spectroscopy of the distal beta-heme pocket VALINE67(E11)-threonine mutation of hemoglobin
Analyse Analysis of the crystal structure, molecular modeling and infrared spectroscopy… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HDB
- Type
- protein
- Length
- 574 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin (deoxy) beta-V67T
- UniProt
- P01922, P02023
- Ligands
- HEM, SO4
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Hemoglobin (deoxy) beta-V67T | protein | 141 | 77% helix, 0% strand | P01922 |
| B, D | Hemoglobin (deoxy) beta-V67T | protein | 146 | 81% helix, 0% strand | P02023 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.75 | 0.87 | 30 | HEM |
| 2 | 492 | 0.75 | 0.83 | 56 | empty |
| 3 | 264 | 0.74 | 0.87 | 32 | HEM |
| 4 | 228 | 0.73 | 0.87 | 26 | HEM |
| 5 | 259 | 0.71 | 0.85 | 29 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 885 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 857 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 707 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 291 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1HDB · Analysis of the crystal structure, molecular modeling and infrared spectroscopy of the… · the same entry in another collection · chain A against A, TM-score 1.00
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 P01922
- Every structure of UniProt P02023
- Elsewhere: RCSB PDB 1HDB · PDBe 1HDB · UniProt P01922 · UniProt P02023
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.