MolNFT v1 · #62125 · protein + DNA
Cprk ocpa DNA complex
3E6C · Cyclic nucleotide-binding protein: “Cprk ocpa DNA complex”. X-ray diffraction, 1 ligand (3C4), 6 pockets (best druggability 0.53). MolNFT v1 #62125 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3E6C
- Type
- protein + DNA
- Length
- 251 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclic nucleotide-binding protein; DNA (5'- D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DG…
- UniProt
- Q18R04
- Ligands
- 3C4
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 39% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cyclic nucleotide-binding protein | protein | 225 | 39% helix, 25% strand | Q18R04 |
| B | DNA (5'- D(P*DGP*DCP*DAP*DTP*DTP*DAP*DAP*DCP*DAP*DTP*DGP*DCP*DC)-3') | dna | 13 | — | — |
| A | DNA (5'- D(P*DGP*DGP*DCP*DAP*DTP*DGP*DTP*DTP*DAP*DAP*DTP*DGP*DC)-3') | dna | 13 | — | — |
Ligands and binding sites
- 3C4 · (3-chloro-4-hydroxyphenyl)acetic acid · ligand · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.53 | 0.88 | 16 | empty |
| 2 | 202 | 0.46 | 0.74 | 34 | empty |
| 3 | 140 | 0.45 | 0.76 | 16 | 3C4 |
| 4 | 104 | 0.38 | 0.75 | 18 | empty |
| 5 | 54 | 0.34 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–A · 579 Ų buried · 47 hydrogen bonds · nucleic-nucleic
- C–B · 419 Ų buried · 10 hydrogen bonds · protein-nucleic
- C–A · 328 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 3E6C · CprK OCPA DNA Complex · 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 Q18R04
- Elsewhere: RCSB PDB 3E6C · PDBe 3E6C · UniProt Q18R04
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