Research workbench
Elk-1/DNA structure reveals how residues distal from DNA- binding surface affect DNA-recognition
Analyse Elk-1/DNA structure reveals how residues distal from DNA- binding surface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DUX
- Type
- protein + DNA
- Length
- 224 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3'); DNA (5'…
- UniProt
- P19419
- Pockets
- 5 · best druggability 0.44
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA (5'- D(*TP*GP*AP*CP*CP*GP*GP*AP*AP*GP*TP*GP*T)-3') | dna | 13 | — | — |
| B, E | DNA (5'- D(*AP*CP*AP*CP*TP*TP*CP*CP*GP*GP*TP*CP*A)-3') | dna | 13 | — | — |
| C, F | Ets-domain protein elk-1 | protein | 86 | 38% helix, 16% strand | P19419 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.44 | 0.77 | 17 | empty |
| 2 | 106 | 0.39 | 0.76 | 17 | empty |
| 3 | 110 | 0.37 | 0.74 | 18 | empty |
| 4 | 75 | 0.28 | 0.72 | 14 | empty |
| 5 | 59 | 0.25 | 0.73 | 14 | empty |
Interfaces
7 interfaces between chains.
- D–E · 574 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- A–B · 571 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- C–F · 509 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 507 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 500 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1DUX · Elk-1/DNA structure reveals how residues distal from DNA-binding surface affect… · the same entry in another collection · chain F against F, TM-score 1.00
- P19419 · AlphaFold monomer V2.0 prediction for ets domain-containing protein elk-1 (P19419) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P19419
- Elsewhere: RCSB PDB 1DUX · PDBe 1DUX · UniProt P19419
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