Research workbench
Crystal structure of the hfq and catalase hpii complex
Analyse Crystal structure of the hfq and catalase hpii complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VU3
- Type
- protein
- Length
- 1,104 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase hpii; Protein hfq
- EC
- 1.11.1.6
- UniProt
- P21179, P0A6X3
- Ligands
- HEM
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase hpii (EC 1.11.1.6) | protein | 727 | 32% helix, 16% strand | P21179 |
| C, H | Protein hfq | protein | 63 | 21% helix, 49% strand | P0A6X3 |
| D | Protein hfq | protein | 63 | 21% helix, 46% strand | P0A6X3 |
| E | Protein hfq | protein | 62 | 21% helix, 48% strand | P0A6X3 |
| F, G | Protein hfq | protein | 63 | 21% helix, 48% strand | P0A6X3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.84 | 0.90 | 72 | empty |
| 2 | 450 | 0.81 | 0.88 | 62 | empty |
| 3 | 317 | 0.78 | 0.89 | 47 | HEM |
| 4 | 140 | 0.55 | 0.82 | 25 | empty |
| 5 | 311 | 0.53 | 0.74 | 32 | empty |
Interfaces
11 interfaces between chains.
- E–F · 768 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 758 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 756 Ų buried · 11 hydrogen bonds · protein-protein
- C–H · 745 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 725 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3VU3 · Crystal structure of the Hfq and catalase HPII complex · the same entry in another collection · chain H against H, TM-score 1.00
- P21179 · AlphaFold monomer V2.0 prediction for catalase hpii (P21179) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P0A6X3 · AlphaFold monomer V2.0 prediction for RNA-binding protein hfq (P0A6X3) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 P21179
- Every structure of UniProt P0A6X3
- Elsewhere: RCSB PDB 3VU3 · PDBe 3VU3 · UniProt P21179 · UniProt P0A6X3
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