Research workbench
Structure determination and refinement of homotetrameric hemoglobin from urechis caupo at 2.5 ångströms resolution
Analyse Structure determination and refinement of homotetrameric hemoglobin from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ITH
- Type
- protein
- Length
- 282 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin (cyano met)
- UniProt
- P06148
- Ligands
- HEM, CYN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hemoglobin (cyano met) | protein | 141 | 77% helix, 0% strand | P06148 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.72 | 0.86 | 32 | CYN, HEM |
| 2 | 233 | 0.70 | 0.85 | 23 | CYN, HEM |
Interfaces
1 interface between chains.
- A–B · 536 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1ITH · Structure determination and refinement of homotetrameric hemoglobin from urechis caupo at… · the same entry in another collection · chain A against A, TM-score 1.00
- P06148 · AlphaFold monomer V2.0 prediction for hemoglobin F-I (P06148) · a predicted model of the same protein · chain A 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 P06148
- Elsewhere: RCSB PDB 1ITH · PDBe 1ITH · UniProt P06148
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