Research workbench
Structure of helicobacter pylori catalase with formic acid bound
Analyse Structure of helicobacter pylori catalase with formic acid bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QWM
- Type
- protein
- Length
- 980 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Kata catalase
- EC
- 1.11.1.6
- UniProt
- P77872
- Ligands
- HEM, AZI
- Pockets
- 15 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Kata catalase (EC 1.11.1.6) | protein | 490 | 35% helix, 17% strand | P77872 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- AZI · Azide ion · ion · chains A, B
- FMT · Formic acid · additive · 36 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.84 | 0.85 | 131 | AZI, HEM, FMT |
| 2 | 382 | 0.64 | 0.78 | 33 | FMT |
| 3 | 474 | 0.63 | 0.76 | 54 | empty |
| 4 | 400 | 0.63 | 0.78 | 35 | FMT |
| 5 | 448 | 0.61 | 0.75 | 53 | FMT |
Interfaces
1 interface between chains.
- A–B · 2397 Ų buried · 37 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 P77872
- Elsewhere: RCSB PDB 1QWM · PDBe 1QWM · UniProt P77872
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