MolNFT v1 · #134299 · protein + DNA
Epstein-barr virus zta DNA binding domain homodimer in complex with methylated DNA
5SZX · DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM)…: “Epstein-barr virus zta DNA binding domain homodimer in complex with methylated DNA”. X-ray diffraction, 1 ligand (PO4), 3 pockets (best druggability 0.72). MolNFT v1 #134299 on GenesisL1: 3D…
- PDB
- 5SZX
- Type
- protein + DNA
- Length
- 160 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM) P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3'); DNA…
- UniProt
- P03206
- Ligands
- PO4
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 74% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'-D(*TP*CP*TP*TP*CP*AP*TP*(5CM) P*GP*CP*TP*CP*AP*GP*TP*GP*CP*T)-3') | dna | 18 | — | — |
| D | DNA (5'-D(*AP*AP*GP*CP*AP*CP*TP*GP*AP*GP*(5CM) P*GP*AP*TP*GP*AP*AP*G)-3') | dna | 18 | — | — |
| A, B | Zta transcription factor | protein | 62 | 74% helix, 0% strand | P03206 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 208 | 0.72 | 0.88 | 25 | empty |
| 2 | 86 | 0.33 | 0.74 | 14 | empty |
| 3 | 101 | 0.33 | 0.73 | 17 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1290 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 769 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- D–B · 378 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–A · 369 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 284 Ų buried · 6 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5SZX · Epstein-Barr virus Zta DNA binding domain homodimer in complex with methylated DNA · the same entry in another collection · chain C against C, TM-score 1.00
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 P03206
- Elsewhere: RCSB PDB 5SZX · PDBe 5SZX · UniProt P03206
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