Research workbench
Crystal structure of the operator-binding form of the multi-drug binding transcriptional repressor cgmr
Analyse Crystal structure of the operator-binding form of the multi-drug binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YVH
- Type
- protein + DNA
- Length
- 742 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator; 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*D…
- UniProt
- Q8NMG3
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Transcriptional regulator | protein | 171 | 70% helix, 0% strand | Q8NMG3 |
| B, D | Transcriptional regulator | protein | 172 | 73% helix, 0% strand | Q8NMG3 |
| E, G | 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*D C)-3' | dna | 14 | — | — |
| F, H | 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*D a)-3' | dna | 14 | — | — |
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 518 | 0.66 | 0.78 | 46 | empty |
| 2 | 518 | 0.66 | 0.77 | 47 | empty |
| 3 | 214 | 0.50 | 0.76 | 23 | empty |
| 4 | 192 | 0.49 | 0.76 | 26 | empty |
| 5 | 116 | 0.35 | 0.73 | 26 | empty |
Interfaces
18 interfaces between chains.
- C–D · 1951 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1947 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 636 Ų buried · 60 hydrogen bonds · nucleic-nucleic
- G–H · 633 Ų buried · 64 hydrogen bonds · nucleic-nucleic
- D–E · 375 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 2YVH · Crystal structure of the operator-binding form of the multi-drug binding transcriptional… · the same entry in another collection · chain E against E, 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 Q8NMG3
- Elsewhere: RCSB PDB 2YVH · PDBe 2YVH · UniProt Q8NMG3
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