Research workbench
Imidazole adduct of the bacterial hemoglobin from vitreoscilla sp.
Analyse Imidazole adduct of the bacterial hemoglobin from vitreoscilla sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VHB
- Type
- protein
- Length
- 270 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (hemoglobin)
- UniProt
- P04252
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 82% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (hemoglobin) | protein | 135 | 82% helix, 0% strand | P04252 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- IMD · Imidazole · additive · 2 copies · chains A, B
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 | 233 | 0.70 | 0.85 | 26 | HEM, IMD |
| 2 | 308 | 0.69 | 0.82 | 23 | empty |
| 3 | 236 | 0.68 | 0.84 | 30 | HEM, IMD |
| 4 | 60 | 0.33 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 454 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
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 P04252
- Elsewhere: RCSB PDB 3VHB · PDBe 3VHB · UniProt P04252
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