MolNFT v1 · #153848 · protein + DNA
Crystal structure of cic-hmg-ETV5-DNA complex
6JRP · Protein capicua homolog: “Crystal structure of cic-hmg-ETV5-DNA complex”. X-ray diffraction, 4 pockets (best druggability 0.65). MolNFT v1 #153848 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6JRP
- Type
- protein + DNA
- Length
- 384 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein capicua homolog; DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3'); DNA…
- UniProt
- Q96RK0
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Protein capicua homolog | protein | 74 | 68% helix, 1% strand | Q96RK0 |
| B, E, H, K | DNA (5'-D(*AP*TP*GP*AP*AP*TP*GP*AP*AP*AP*A)-3') | dna | 11 | — | — |
| C, F, I, L | DNA (5'-D(*TP*TP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3') | dna | 11 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.65 | 0.92 | 15 | empty |
| 2 | 56 | 0.57 | 0.90 | 15 | empty |
| 3 | 68 | 0.47 | 0.84 | 15 | empty |
| 4 | 63 | 0.43 | 0.82 | 11 | empty |
Interfaces
26 interfaces between chains.
- J–L · 751 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–F · 727 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–C · 714 Ų buried · 12 hydrogen bonds · protein-nucleic
- J–K · 682 Ų buried · 8 hydrogen bonds · protein-nucleic
- G–I · 669 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 modified, 2 disulfide (engineered, disulfide).
Compared structures
- 6JRP · Crystal structure of CIC-HMG-ETV5-DNA complex · the same entry in another collection · chain L against L, 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 Q96RK0
- Elsewhere: RCSB PDB 6JRP · PDBe 6JRP · UniProt Q96RK0
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