MolNFT v1 · #109663 · protein + DNA
Egr-1 with doubly methylated DNA
4X9J · Early growth response protein 1: “Egr-1 with doubly methylated DNA”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.60). MolNFT v1 #109663 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4X9J
- Type
- protein + DNA
- Length
- 108 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Early growth response protein 1; DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3')…
- UniProt
- P18146
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Early growth response protein 1 | protein | 86 | 41% helix, 14% strand | P18146 |
| B | DNA (5'-D(*AP*GP*(5CM)P*GP*TP*GP*GP*GP*(5CM)P*GP*T)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*(5CM)P*GP*C)-3') | dna | 11 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.60 | 0.88 | 18 | empty |
| 2 | 52 | 0.56 | 0.91 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 965 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–C · 551 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–C · 480 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
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 P18146
- Elsewhere: RCSB PDB 4X9J · PDBe 4X9J · UniProt P18146
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