Research workbench
Crystal structure of zmasch Y47F mutant protein from zymomonas mobilis
Analyse Crystal structure of zmasch Y47F mutant protein from zymomonas mobilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y6B
- Type
- protein
- Length
- 566 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Helix-turn-helix domain-containing protein
- UniProt
- A0A0H3G0N3
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Helix-turn-helix domain-containing protein | protein | 145 | 31% helix, 34% strand | A0A0H3G0N3 |
| B, C | Helix-turn-helix domain-containing protein | protein | 141 | 30% helix, 36% strand | A0A0H3G0N3 |
| D | Helix-turn-helix domain-containing protein | protein | 139 | 30% helix, 36% strand | A0A0H3G0N3 |
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 | 607 | 0.68 | 0.77 | 68 | empty |
| 2 | 327 | 0.67 | 0.81 | 38 | empty |
| 3 | 162 | 0.53 | 0.79 | 17 | empty |
| 4 | 136 | 0.48 | 0.78 | 19 | empty |
| 5 | 123 | 0.46 | 0.78 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–B · 705 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 576 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 366 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 77 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5Y6B · Crystal structure of ZmASCH Y47F mutant protein from Zymomonas mobilis · 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 A0A0H3G0N3
- Elsewhere: RCSB PDB 5Y6B · PDBe 5Y6B · UniProt A0A0H3G0N3
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