MolNFT v1 · #97317 · protein + DNA
Crystal structure of a proteolytically defined zbeta domain of human dai (ZBP1, dlm-1)
4KA4 · Z-DNA-binding protein 1: “Crystal structure of a proteolytically defined zbeta domain of human dai (ZBP1, dlm-1)”. X-ray diffraction, 3 pockets (best druggability 0.65). MolNFT v1 #97317 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4KA4
- Type
- protein + DNA
- Length
- 263 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Z-DNA-binding protein 1; DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3')
- UniProt
- Q9H171
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Z-DNA-binding protein 1 | protein | 61 | 41% helix, 16% strand | Q9H171 |
| B, E | Z-DNA-binding protein 1 | protein | 59 | 54% helix, 17% strand | Q9H171 |
| D | Z-DNA-binding protein 1 | protein | 60 | 50% helix, 17% strand | Q9H171 |
| C, F, G, H | DNA (5'-D(*TP*CP*GP*CP*GP*CP*G)-3') | dna | 6 | — | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.65 | 0.78 | 37 | empty |
| 2 | 490 | 0.63 | 0.76 | 34 | empty |
| 3 | 159 | 0.49 | 0.78 | 22 | empty |
Interfaces
17 interfaces between chains.
- A–C · 362 Ų buried · 6 hydrogen bonds · protein-nucleic
- E–F · 343 Ų buried · 7 hydrogen bonds · protein-nucleic
- C–H · 335 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- D–H · 333 Ų buried · 8 hydrogen bonds · protein-nucleic
- F–G · 322 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 4KA4 · Crystal structure of a proteolytically defined Zbeta domain of human DAI (ZBP1, DLM-1) · the same entry in another collection · chain H against H, TM-score 1.00
- Q9H171 · AlphaFold monomer V2.0 prediction for Z-DNA-binding protein 1 (Q9H171) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q9H171
- Elsewhere: RCSB PDB 4KA4 · PDBe 4KA4 · UniProt Q9H171
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