MolNFT v1 · #134563 · protein + DNA
Crystal structure of hhv-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA
5T7X · DNA (5'- D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*…: “Crystal structure of hhv-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal carcinoma) bound to DNA”. X-ray diffraction, 2 pockets (best druggability 0.50).…
- PDB
- 5T7X
- Type
- protein + DNA
- Length
- 332 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3'); DNA (5'…
- UniProt
- Q3KSS4
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA (5'- D(*GP*GP*AP*TP*AP*GP*CP*CP*TP*AP*TP*GP*CP*TP*AP*CP*CP*C)-3') | dna | 18 | — | — |
| D | DNA (5'- D(*GP*GP*GP*TP*AP*GP*CP*AP*TP*AP*GP*GP*CP*TP*AP*TP*CP*C)-3') | dna | 18 | — | — |
| A | Epstein-barr nuclear antigen 1 | protein | 147 | 32% helix, 26% strand | Q3KSS4 |
| B | Epstein-barr nuclear antigen 1 | protein | 149 | 33% helix, 26% strand | Q3KSS4 |
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 | 139 | 0.50 | 0.79 | 26 | empty |
| 2 | 146 | 0.48 | 0.78 | 25 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2250 Ų buried · 34 hydrogen bonds · protein-protein
- D–B · 857 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 799 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- C–A · 758 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–B · 727 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5T7X · Crystal structure of HHV-4 EBNA1 DNA binding domain (patient-derived, nasopharyngeal… · the same entry in another collection · chain B against B, 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 Q3KSS4
- Elsewhere: RCSB PDB 5T7X · PDBe 5T7X · UniProt Q3KSS4
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