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Crystal structure of vibrio salmonicida catalase
Analyse Crystal structure of vibrio salmonicida catalase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ISA
- Type
- protein
- Length
- 3,856 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- Q3LSM1
- Ligands
- HEM, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Catalase (EC 1.11.1.6) | protein | 482 | 34% helix, 18% strand | Q3LSM1 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 8 copies · chains A, C, B, D, E, G, F, H
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 | 738 | 0.87 | 0.91 | 48 | CL |
| 2 | 758 | 0.87 | 0.90 | 54 | CL |
| 3 | 294 | 0.86 | 0.96 | 43 | HEM |
| 4 | 284 | 0.85 | 0.96 | 42 | HEM |
| 5 | 301 | 0.85 | 0.96 | 41 | HEM |
Interfaces
16 interfaces between chains.
- A–B · 4583 Ų buried · 77 hydrogen bonds · protein-protein
- E–F · 4582 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 4557 Ų buried · 78 hydrogen bonds · protein-protein
- G–H · 4553 Ų buried · 75 hydrogen bonds · protein-protein
- A–C · 4210 Ų buried · 57 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (oxidation).
Compared structures
- 2ISA · Crystal Structure of Vibrio salmonicida catalase · the same entry in another collection · chain D against D, 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 Q3LSM1
- Elsewhere: RCSB PDB 2ISA · PDBe 2ISA · UniProt Q3LSM1
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