Research workbench
Crystal structure of catalase hpii from escherichia COLI, native structure at 1.9 a resolution.
Analyse Crystal structure of catalase hpii from escherichia COLI, native structure at… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GGE
- Type
- protein
- Length
- 2,908 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (catalase hpii)
- EC
- 1.11.1.6
- UniProt
- P21179
- Ligands
- HDD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Protein (catalase hpii) (EC 1.11.1.6) | protein | 727 | 32% helix, 18% strand | P21179 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.89 | 0.96 | 58 | empty |
| 2 | 485 | 0.89 | 0.96 | 54 | empty |
| 3 | 360 | 0.85 | 0.94 | 43 | empty |
| 4 | 249 | 0.84 | 0.96 | 35 | HDD |
| 5 | 238 | 0.84 | 0.96 | 35 | HDD |
Interfaces
6 interfaces between chains.
- A–D · 6205 Ų buried · 124 hydrogen bonds · protein-protein
- B–C · 6150 Ų buried · 120 hydrogen bonds · protein-protein
- B–D · 5957 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 5919 Ų buried · 86 hydrogen bonds · protein-protein
- C–D · 2277 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 1GGE · Crystal structure of catalase hpii from escherichia COLI, native structure at 1.9 a… · the same entry in another collection · chain D against D, TM-score 1.00
- P21179 · AlphaFold monomer V2.0 prediction for catalase hpii (P21179) · a predicted model of the same protein · chain B 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 P21179
- Elsewhere: RCSB PDB 1GGE · PDBe 1GGE · UniProt P21179
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