Research workbench
Structure of the third kh domain of hnrnp K in complex with 15-mer ssdna
Analyse Structure of the third kh domain of hnrnp K in complex with 15-mer ssdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZZJ
- Type
- protein + DNA
- Length
- 230 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*TP*TP*T)-3'; Heterogeneous nuclear…
- UniProt
- P61978
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 5'-D(*TP*TP*CP*CP*CP*CP*TP*CP*CP*CP*CP*AP*TP*TP*T)-3' | dna | 8 | — | — |
| A | Heterogeneous nuclear ribonucleoprotein K | protein | 75 | 49% helix, 27% strand | P61978 |
| B | Heterogeneous nuclear ribonucleoprotein K | protein | 73 | 48% helix, 27% strand | P61978 |
| C | Heterogeneous nuclear ribonucleoprotein K | protein | 74 | 47% helix, 27% strand | P61978 |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.47 | 0.80 | 23 | empty |
| 2 | 105 | 0.37 | 0.74 | 20 | empty |
| 3 | 95 | 0.35 | 0.74 | 19 | empty |
Interfaces
4 interfaces between chains.
- D–B · 527 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–A · 486 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–C · 482 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 66 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1ZZJ · Structure of the third KH domain of hnRNP K in complex with 15-mer ssDNA · the same entry in another collection · chain D against D, TM-score 1.00
- P61978 · AlphaFold monomer V2.0 prediction for heterogeneous nuclear ribonucleoprotein K (P61978) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P61978
- Elsewhere: RCSB PDB 1ZZJ · PDBe 1ZZJ · UniProt P61978
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