Research workbench
Ligand-free structure of CYP142 from mycobacterium smegmatis
Analyse Ligand-free structure of CYP142 from mycobacterium smegmatis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZBY
- Type
- protein
- Length
- 2,414 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- P450 heme-thiolate protein
- UniProt
- A0R4Q6
- Ligands
- HEM, GLC, SO4
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F | P450 heme-thiolate protein | protein | 402 | 52% helix, 10% strand | A0R4Q6 |
| B | P450 heme-thiolate protein | protein | 404 | 53% helix, 9% strand | A0R4Q6 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 6 copies · chains A, B, C, D, E, F
- GLC · alpha-D-glucopyranose · sugar · 42 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 17 copies · chains A, B, C, D, E, F
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 558 | 0.83 | 0.89 | 68 | HEM, EDO |
| 2 | 508 | 0.83 | 0.89 | 61 | HEM, EDO |
| 3 | 499 | 0.83 | 0.89 | 64 | HEM, EDO |
| 4 | 514 | 0.83 | 0.89 | 66 | HEM, EDO |
| 5 | 519 | 0.83 | 0.89 | 66 | HEM, EDO |
Interfaces
5 interfaces between chains.
- C–F · 861 Ų buried · 14 hydrogen bonds · protein-protein
- B–E · 855 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 590 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 91 Ų buried · 0 hydrogen bonds · protein-protein
- C–E · 85 Ų buried · 0 hydrogen bonds · protein-protein
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 A0R4Q6
- Elsewhere: RCSB PDB 3ZBY · PDBe 3ZBY · UniProt A0R4Q6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.