Research workbench
Crystal structure of the imidazole-bound form of the HGBRL'S globin domain
Analyse Crystal structure of the imidazole-bound form of the HGBRL'S globin domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WFX
- Type
- protein
- Length
- 271 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemoglobin-like flavoprotein fused to ROADBLOCK/LC7 domain
- UniProt
- B3DUZ1
- Ligands
- HEM
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 89% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemoglobin-like flavoprotein fused to ROADBLOCK/LC7 domain | protein | 136 | 90% helix, 0% strand | B3DUZ1 |
| B | Hemoglobin-like flavoprotein fused to ROADBLOCK/LC7 domain | protein | 135 | 88% helix, 0% strand | B3DUZ1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- HEZ · Hexane-1,6-diol · additive · 6 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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 330 | 0.74 | 0.85 | 29 | IMD, HEM |
| 2 | 355 | 0.72 | 0.83 | 35 | HEM, IMD |
| 3 | 449 | 0.67 | 0.79 | 37 | HEZ |
Interfaces
1 interface between chains.
- A–B · 2662 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3WFX · Crystal Structure of the Imidazole-Bound Form of the HGbRL's Globin Domain · 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 B3DUZ1
- Elsewhere: RCSB PDB 3WFX · PDBe 3WFX · UniProt B3DUZ1
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