MolNFT v1 · #8286 · protein
Compound II structure of micrococcus lysodeikticus catalase
1GWF: “Compound II structure of micrococcus lysodeikticus catalase”. X-ray diffraction, 3 ligands (HEM, SO4, O), 6 pockets (best druggability 0.76). MolNFT v1 #8286 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1GWF
- Type
- protein
- Length
- 498 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- P29422
- Ligands
- HEM, SO4, O
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase (EC 1.11.1.6) | protein | 498 | 31% helix, 16% strand | P29422 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- O · Oxygen atom · ion · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.76 | 0.87 | 41 | HEM, O |
| 2 | 230 | 0.57 | 0.79 | 32 | SO4 |
| 3 | 248 | 0.51 | 0.76 | 33 | empty |
| 4 | 50 | 0.34 | 0.79 | 14 | empty |
| 5 | 85 | 0.33 | 0.74 | 19 | empty |
Modifications
Observed in the structure: 5 modified (nonstandard).
Compared structures
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 P29422
- Elsewhere: RCSB PDB 1GWF · PDBe 1GWF · UniProt P29422
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