Research workbench
Tcar-ssdna complex crystal structure reveals the novel ssdna binding mechanism of the marr family proteins
Analyse Tcar-ssdna complex crystal structure reveals the novel ssdna binding mechanism… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KDP
- Type
- protein + DNA
- Length
- 1,077 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tcar transcription regulator; DNA (5'- D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*…
- UniProt
- Q8CN94
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G | Tcar transcription regulator | protein | 151 | 60% helix, 0% strand | Q8CN94 |
| E | Tcar transcription regulator | protein | 150 | 55% helix, 1% strand | Q8CN94 |
| H | DNA (5'- D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3') | dna | 11 | — | — |
| J | DNA (5'- D(*CP*GP*CP*AP*GP*CP*GP*CP*GP*CP*AP*GP*CP*CP*CP*TP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, D, E, H
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.87 | 0.88 | 106 | empty |
| 2 | 310 | 0.82 | 0.92 | 40 | empty |
| 3 | 1126 | 0.81 | 0.83 | 90 | empty |
| 4 | 333 | 0.81 | 0.91 | 41 | empty |
| 5 | 1054 | 0.81 | 0.82 | 88 | empty |
Interfaces
20 interfaces between chains.
- A–B · 3255 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 3096 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 3004 Ų buried · 22 hydrogen bonds · protein-protein
- C–G · 718 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 477 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4KDP · TcaR-ssDNA complex crystal structure reveals the novel ssDNA binding mechanism of the… · the same entry in another collection · chain C against C, 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 Q8CN94
- Elsewhere: RCSB PDB 4KDP · PDBe 4KDP · UniProt Q8CN94
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