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Crystal structure of catalase hpii from escherichia COLI (serendipitously crystallized)
Analyse Crystal structure of catalase hpii from escherichia COLI (serendipitously… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZTV
- Type
- protein
- Length
- 2,904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase hpii
- EC
- 1.11.1.6
- UniProt
- P21179
- Ligands
- HDD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase hpii (EC 1.11.1.6) | protein | 726 | 31% helix, 18% strand | P21179 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, D, B, C
- GOL · Glycerol · additive · chains B
- EDO · 1,2-ethanediol · additive · chains 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.89 | 0.96 | 60 | empty |
| 2 | 507 | 0.89 | 0.96 | 60 | empty |
| 3 | 389 | 0.86 | 0.94 | 46 | empty |
| 4 | 309 | 0.85 | 0.95 | 50 | HDD |
| 5 | 287 | 0.85 | 0.95 | 50 | HDD |
Interfaces
6 interfaces between chains.
- A–D · 6230 Ų buried · 115 hydrogen bonds · protein-protein
- B–C · 6198 Ų buried · 121 hydrogen bonds · protein-protein
- B–D · 5910 Ų buried · 82 hydrogen bonds · protein-protein
- A–C · 5888 Ų buried · 82 hydrogen bonds · protein-protein
- C–D · 2284 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6ZTV · Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized) · 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 6ZTV · PDBe 6ZTV · UniProt P21179
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