MolNFT v1 · #82358 · protein + DNA
Contribution of the first K-homology domain of POLY(C)-binding protein 1 to its affinity and specificity for C-rich oligonucleotides
3VKE · POLY(RC)-binding protein 1: “Contribution of the first K-homology domain of POLY(C)-binding protein 1 to its affinity and specificity for…”. X-ray diffraction, 4 pockets (best druggability 0.41). MolNFT v1 #82358 on GenesisL1: 3D…
- PDB
- 3VKE
- Type
- protein + DNA
- Length
- 313 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POLY(RC)-binding protein 1; DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3')
- UniProt
- Q15365
- Pockets
- 4 · best druggability 0.41
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POLY(RC)-binding protein 1 | protein | 76 | 50% helix, 29% strand | Q15365 |
| B | POLY(RC)-binding protein 1 | protein | 75 | 56% helix, 27% strand | Q15365 |
| C | POLY(RC)-binding protein 1 | protein | 70 | 54% helix, 29% strand | Q15365 |
| D | POLY(RC)-binding protein 1 | protein | 72 | 54% helix, 28% strand | Q15365 |
| R, S | DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3') | dna | 6 | — | — |
| T, U | DNA (5'-D(P*AP*CP*CP*CP*CP*A)-3') | dna | 4 | — | — |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.41 | 0.75 | 20 | empty |
| 2 | 50 | 0.40 | 0.82 | 14 | empty |
| 3 | 109 | 0.37 | 0.75 | 16 | empty |
| 4 | 111 | 0.37 | 0.74 | 17 | empty |
Interfaces
10 interfaces between chains.
- A–C · 989 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 965 Ų buried · 10 hydrogen bonds · protein-protein
- A–R · 685 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–S · 629 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–T · 551 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 3VKE · Contribution of the first K-homology domain of poly(C)-binding protein 1 to its affinity… · the same entry in another collection · chain U against U, TM-score 1.00
- Q15365 · AlphaFold monomer V2.0 prediction for POLY(RC)-binding protein 1 (Q15365) · a predicted model of the same protein · chain C against A, TM-score 0.96
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 Q15365
- Elsewhere: RCSB PDB 3VKE · PDBe 3VKE · UniProt Q15365
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