Research workbench
Crystallographic structure of (hbii-hbiii)-O2 from lucina pectinata at pH 7.0
Analyse Crystallographic structure of (hbii-hbiii)-O2 from lucina pectinata at pH 7.0 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OTX
- 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, P41262
- Ligands
- HEM, OXY
- Pockets
- 1 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin II | protein | 151 | 75% helix, 0% strand | Q86G74 |
| B | Hemoglobin III | protein | 152 | 76% helix, 0% strand | P41262 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- OXY · Oxygen molecule · ion · 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 | 1108 | 0.84 | 0.85 | 76 | HEM, OXY |
Interfaces
1 interface between chains.
- A–B · 844 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6OTX · Crystallographic Structure of (HbII-HbIII)-O2 from Lucina pectinata at pH 7.0 · the same entry in another collection · chain A against A, TM-score 1.00
- P41262 · AlphaFold monomer V2.0 prediction for hemoglobin-3 (P41262) · 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 Q86G74
- Every structure of UniProt P41262
- Elsewhere: RCSB PDB 6OTX · PDBe 6OTX · UniProt Q86G74 · UniProt P41262
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