MolNFT v1 · #140043 · protein
Catpo mutant - V536W
5XY4 · Catalase: “Catpo mutant - V536W”. X-ray diffraction, 2 ligands (HDD, CA), 20 pockets (best druggability 0.87). MolNFT v1 #140043 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XY4
- Type
- protein
- Length
- 2,712 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- M4GGR7
- Ligands
- HDD, CA
- 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 | Catalase (EC 1.11.1.6) | protein | 678 | 34% helix, 18% strand | M4GGR7 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, C, B, D
- CA · Calcium ion · metal · 10 copies · chains A, B, C, D
- P6G · Hexaethylene glycol · additive · chains C
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 | 477 | 0.87 | 0.94 | 94 | CA |
| 2 | 271 | 0.86 | 0.97 | 49 | HDD |
| 3 | 1100 | 0.85 | 0.86 | 120 | CA |
| 4 | 1113 | 0.85 | 0.86 | 120 | CA |
| 5 | 359 | 0.85 | 0.94 | 52 | CA |
Interfaces
6 interfaces between chains.
- B–D · 5816 Ų buried · 83 hydrogen bonds · protein-protein
- A–C · 5762 Ų buried · 85 hydrogen bonds · protein-protein
- B–C · 5114 Ų buried · 69 hydrogen bonds · protein-protein
- A–D · 5098 Ų buried · 70 hydrogen bonds · protein-protein
- C–D · 2060 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5XY4 · CATPO mutant - V536W · the same entry in another collection · 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 M4GGR7
- Elsewhere: RCSB PDB 5XY4 · PDBe 5XY4 · UniProt M4GGR7
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