Research workbench
Crystal structure analysis of the SER305ALA variant of katg from haloarcula marismortui complexes with inhibitor sha
Analyse Crystal structure analysis of the SER305ALA variant of katg from haloarcula… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VLL
- Type
- protein
- Length
- 1,413 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, SHA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-peroxidase 2 (EC 1.11.1.21) | protein | 703 | 46% helix, 6% strand | O59651 |
| B | Catalase-peroxidase 2 (EC 1.11.1.21) | protein | 710 | 44% helix, 7% strand | O59651 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- SHA · Salicylhydroxamic acid · ligand · 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 | 642 | 0.84 | 0.88 | 67 | HEM, SHA |
| 2 | 767 | 0.84 | 0.87 | 120 | empty |
| 3 | 762 | 0.83 | 0.86 | 76 | HEM, SHA |
| 4 | 772 | 0.82 | 0.85 | 94 | empty |
| 5 | 445 | 0.77 | 0.86 | 61 | empty |
Interfaces
1 interface between chains.
- A–B · 4199 Ų buried · 52 hydrogen bonds · protein-protein
Compared structures
- 3VLL · Crystal Structure Analysis of the Ser305Ala variant of KatG from HALOARCULA MARISMORTUI… · 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 0.99
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 3VLL · PDBe 3VLL · UniProt O59651
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