MolNFT v1 · #23803 · protein + DNA
Co-crystal structure of human YY1 zinc finger domain bound to the adeno-associated virus P5 initiator element
1UBD · DNA (5'- D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*…: “Co-crystal structure of human YY1 zinc finger domain bound to the adeno-associated virus P5 initiator element”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best…
- PDB
- 1UBD
- Type
- protein + DNA
- Length
- 154 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*A P*GP*CP*G)-3'); DNA (5'…
- UniProt
- P25490
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*AP*GP*GP*GP*TP*CP*TP*CP*CP*AP*TP*TP*TP*TP*GP*AP*A P*GP*CP*G)-3') | dna | 20 | — | — |
| B | DNA (5'- D(*CP*GP*CP*TP*TP*CP*AP*AP*AP*AP*TP*GP*GP*AP*GP*AP*C P*CP*CP*T)-3') | dna | 20 | — | — |
| C | Protein (YY1 zinc finger domain) | protein | 114 | 35% helix, 11% strand | P25490 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.57 | 0.80 | 34 | empty |
| 2 | 89 | 0.55 | 0.86 | 17 | empty |
| 3 | 100 | 0.42 | 0.78 | 15 | empty |
| 4 | 81 | 0.42 | 0.79 | 21 | empty |
| 5 | 66 | 0.27 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1008 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–B · 876 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–C · 556 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1UBD · Co-crystal structure of human YY1 zinc finger domain bound to the adeno-associated virus… · the same entry in another collection · chain A against A, TM-score 1.00
- P25490 · AlphaFold monomer V2.0 prediction for transcriptional repressor protein YY1 (P25490) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P25490
- Elsewhere: RCSB PDB 1UBD · PDBe 1UBD · UniProt P25490
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