Research workbench
DNA-bound form of tetr-like repressor simr
Analyse DNA-bound form of tetr-like repressor simr in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZQL
- Type
- protein + DNA
- Length
- 992 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative repressor SIMREG2; 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP…
- UniProt
- Q9AMH9
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Putative repressor SIMREG2 | protein | 236 | 69% helix, 0% strand | Q9AMH9 |
| B, D | Putative repressor SIMREG2 | protein | 226 | 71% helix, 0% strand | Q9AMH9 |
| E, G | 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*CP*CP*GP*TP*AP*DCP *GP*AP*A)-3' | dna | 17 | — | — |
| F, H | 5'-D(*DTP*TP*CP*GP*TP*AP*CP*GP*GP*CP*GP*TP*AP*DCP *GP*AP*A)-3' | dna | 17 | — | — |
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 579 | 0.86 | 0.91 | 51 | empty |
| 2 | 816 | 0.85 | 0.88 | 62 | empty |
| 3 | 900 | 0.85 | 0.87 | 71 | empty |
| 4 | 515 | 0.85 | 0.90 | 59 | empty |
| 5 | 1119 | 0.76 | 0.78 | 76 | empty |
Interfaces
13 interfaces between chains.
- A–B · 2807 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2720 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 760 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- E–F · 756 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–F · 406 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 3ZQL · DNA-bound form of TetR-like repressor SimR · 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 Q9AMH9
- Elsewhere: RCSB PDB 3ZQL · PDBe 3ZQL · UniProt Q9AMH9
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