Research workbench
Azide adduct of the bacterial hemoglobin from vitreoscilla stercoraria
Analyse Azide adduct of the bacterial hemoglobin from vitreoscilla stercoraria in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VHB
- Type
- protein
- Length
- 274 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin
- UniProt
- P04252
- Ligands
- HEM, AZI
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 86% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin | protein | 137 | 87% helix, 0% strand | P04252 |
| B | Hemoglobin | protein | 137 | 85% helix, 0% strand | P04252 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- AZI · Azide ion · ion · 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 | 365 | 0.69 | 0.81 | 28 | empty |
| 2 | 251 | 0.69 | 0.84 | 31 | AZI, HEM |
| 3 | 247 | 0.68 | 0.84 | 31 | AZI, HEM |
| 4 | 118 | 0.47 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 398 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2VHB · Azide adduct of the bacterial hemoglobin from vitreoscilla stercoraria · the same entry in another collection · chain A against A, TM-score 1.00
- P04252 · AlphaFold monomer V2.0 prediction for bacterial hemoglobin (P04252) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 2VHB · PDBe 2VHB · UniProt P04252
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