MolNFT v1 · #82396 · protein
Crystal structure analysis of the SER305ALA variant of katg from haloarcula marismortui complexes with inhibitor sha
3VLL · Catalase-peroxidase 2: “Crystal structure analysis of the SER305ALA variant of katg from haloarcula marismortui complexes with…”. X-ray diffraction, 2 ligands (HEM, SHA), 20 pockets (best druggability 0.84). MolNFT v1 #82396 on…
- 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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