Research workbench
Crystal structure analysis of the cyanide ARG409LEU variant katg from haloarcula marismortui
Analyse Crystal structure analysis of the cyanide ARG409LEU variant katg from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VLI
- Type
- protein
- Length
- 1,425 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-peroxidase 2
- EC
- 1.11.1.21
- UniProt
- O59651
- Ligands
- HEM, CYN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-peroxidase 2 (EC 1.11.1.21) | protein | 711 | 46% helix, 8% strand | O59651 |
| B | Catalase-peroxidase 2 (EC 1.11.1.21) | protein | 714 | 46% helix, 7% strand | O59651 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- CYN · Cyanide ion · ion · 2 copies · chains A, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.83 | 0.84 | 119 | empty |
| 2 | 644 | 0.83 | 0.87 | 72 | HEM, CYN |
| 3 | 572 | 0.83 | 0.88 | 73 | HEM, CYN |
| 4 | 986 | 0.80 | 0.82 | 79 | empty |
| 5 | 649 | 0.78 | 0.84 | 74 | empty |
Interfaces
1 interface between chains.
- A–B · 3866 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 3VLI · Crystal Structure Analysis of the Cyanide Arg409Leu Variant KatG from HALOARCULA… · the same entry in another collection · chain A against A, TM-score 1.00
- O59651 · AlphaFold monomer V2.0 prediction for catalase-peroxidase 2 (O59651) · a predicted model of the same protein · chain A 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 O59651
- Elsewhere: RCSB PDB 3VLI · PDBe 3VLI · UniProt O59651
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