Research workbench
Oxygen-bound HELL'S gate globin I by lb nanotemplate method
Analyse Oxygen-bound HELL'S gate globin I by lb nanotemplate method in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UBC
- Type
- protein
- Length
- 393 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-like flavoprotein
- UniProt
- B3DUZ7
- Ligands
- HEM, OXY
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 87% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G | Hemoglobin-like flavoprotein | protein | 131 | 87% helix, 0% strand | B3DUZ7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, D, G
- OXY · Oxygen molecule · ion · 3 copies · chains A, D, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.76 | 0.87 | 35 | HEM, OXY |
| 2 | 320 | 0.75 | 0.86 | 37 | HEM, OXY |
| 3 | 307 | 0.75 | 0.86 | 32 | HEM, OXY |
| 4 | 69 | 0.32 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–D · 786 Ų buried · 11 hydrogen bonds · protein-protein
- A–G · 545 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3UBC · Oxygen-bound hell's gate globin I by LB nanotemplate method · 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 B3DUZ7
- Elsewhere: RCSB PDB 3UBC · PDBe 3UBC · UniProt B3DUZ7
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