MolNFT v1 · #30300 · protein + DNA
Crystal structure analysis of the third kh domain of hnrnp K in complex with ssdna
1ZZI · 5'-D(*CP*TP*CP*CP*CP*C)-3': “Crystal structure analysis of the third kh domain of hnrnp K in complex with ssdna”. X-ray diffraction, 2 pockets (best druggability 0.35). MolNFT v1 #30300 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1ZZI
- Type
- protein + DNA
- Length
- 172 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*TP*CP*CP*CP*C)-3'; Heterogeneous nuclear ribonucleoprotein K
- UniProt
- P61978
- Pockets
- 2 · best druggability 0.35
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*CP*TP*CP*CP*CP*C)-3' | dna | 6 | — | — |
| D | 5'-D(*CP*TP*CP*CP*CP*C)-3' | dna | 5 | — | — |
| A | Heterogeneous nuclear ribonucleoprotein K | protein | 82 | 45% helix, 24% strand | P61978 |
| B | Heterogeneous nuclear ribonucleoprotein K | protein | 79 | 48% helix, 25% strand | P61978 |
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 60 | 0.35 | 0.77 | 14 | empty |
| 2 | 60 | 0.31 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–A · 531 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–B · 505 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 440 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1ZZI · Crystal Structure Analysis of the third KH domain of hnRNP K in complex with ssDNA · the same entry in another collection · chain C against C, TM-score 1.00
- P61978 · AlphaFold monomer V2.0 prediction for heterogeneous nuclear ribonucleoprotein K (P61978) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 1ZZI · PDBe 1ZZI · UniProt P61978
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