Research workbench
Structure of hbii-III-cn from lucina pectinata at pH 5.0
Analyse Structure of hbii-III-cn from lucina pectinata at pH 5.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PT8
- Type
- protein
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin II; Hemoglobin III
- UniProt
- Q86G74, A7UAU9
- Ligands
- HEM, ACE, CYN
- Pockets
- 1 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin II | protein | 151 | 78% helix, 0% strand | Q86G74 |
| B | Hemoglobin III | protein | 152 | 76% helix, 0% strand | A7UAU9 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- ACE · Acetyl group · ligand · chains A
- CYN · Cyanide ion · ion · 2 copies · chains A, B
- FMT · Formic acid · additive · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1168 | 0.84 | 0.85 | 78 | HEM, CYN, GOL, FMT |
Interfaces
1 interface between chains.
- A–B · 830 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 3PT8 · Structure of HbII-III-CN from Lucina pectinata at pH 5.0 · 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 Q86G74
- Every structure of UniProt A7UAU9
- Elsewhere: RCSB PDB 3PT8 · PDBe 3PT8 · UniProt Q86G74 · UniProt A7UAU9
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