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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
- 6ZTW
- Type
- protein
- Length
- 5,809 residues
- Chains
- 8
- 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 · 2 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H | Catalase hpii (EC 1.11.1.6) | protein | 726 | 32% helix, 18% strand | P21179 |
| G | Catalase hpii (EC 1.11.1.6) | protein | 727 | 31% helix, 18% strand | P21179 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 9 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, D, C, E, F
- GOL · Glycerol · additive · 6 copies · chains A, B, C, E, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 511 | 0.89 | 0.96 | 56 | empty |
| 2 | 510 | 0.89 | 0.96 | 61 | empty |
| 3 | 509 | 0.89 | 0.96 | 55 | empty |
| 4 | 487 | 0.89 | 0.96 | 56 | empty |
| 5 | 385 | 0.86 | 0.94 | 46 | empty |
Interfaces
15 interfaces between chains.
- F–G · 6347 Ų buried · 123 hydrogen bonds · protein-protein
- A–D · 6264 Ų buried · 119 hydrogen bonds · protein-protein
- B–C · 6256 Ų buried · 122 hydrogen bonds · protein-protein
- E–H · 6241 Ų buried · 120 hydrogen bonds · protein-protein
- E–G · 5916 Ų buried · 82 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 6ZTW · Crystal Structure of catalase HPII from Escherichia coli (serendipitously crystallized) · the same entry in another collection · chain G against G, TM-score 1.00
- P21179 · AlphaFold monomer V2.0 prediction for catalase hpii (P21179) · a predicted model of the same protein · chain G 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 6ZTW · PDBe 6ZTW · UniProt P21179
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