MolNFT v1 · #92800 · protein + DNA
Crystal structure of the tal effector DHAX3 bound to dsdna containing repetitive methyl-cpg
4GJP: “Crystal structure of the tal effector DHAX3 bound to dsdna containing repetitive methyl-cpg”. X-ray diffraction, 1 ligand (MG), 7 pockets (best druggability 0.78). MolNFT v1 #92800 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4GJP
- Type
- protein + DNA
- Length
- 1,051 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- HAX3; DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*(5CM) P*GP*TP*CP*TP*CP*T)-3'); DNA…
- UniProt
- Q3ZD72
- Ligands
- MG
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HAX3 | protein | 497 | 74% helix, 0% strand | Q3ZD72 |
| I | DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*(5CM) P*GP*TP*CP*TP*CP*T)-3') | dna | 17 | — | — |
| J | DNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3') | dna | 17 | — | — |
| B | HAX3 | protein | 489 | 72% helix, 0% strand | Q3ZD72 |
| G | DNA (5'-D(*TP*GP*TP*CP*CP*CP*TP*TP*(5CM)P*GP*(5CM) P*GP*TP*CP*TP*CP*T)-3') | dna | 15 | — | — |
| H | DNA (5'- D(*AP*GP*AP*GP*AP*CP*GP*CP*GP*AP*AP*GP*GP*GP*AP*CP*A)-3') | dna | 16 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, J, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1195 | 0.78 | 0.80 | 112 | MG |
| 2 | 459 | 0.72 | 0.83 | 57 | empty |
| 3 | 364 | 0.65 | 0.80 | 44 | MG |
| 4 | 240 | 0.54 | 0.77 | 27 | empty |
| 5 | 67 | 0.47 | 0.83 | 18 | empty |
Interfaces
10 interfaces between chains.
- A–I · 1731 Ų buried · 24 hydrogen bonds · protein-nucleic
- B–G · 1665 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 923 Ų buried · 8 hydrogen bonds · protein-protein
- I–J · 772 Ų buried · 65 hydrogen bonds · nucleic-nucleic
- G–H · 670 Ų buried · 62 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 4GJP · Crystal structure of the TAL effector dHax3 bound to dsDNA containing repetitive… · the same entry in another collection · chain A against A, 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 Q3ZD72
- Elsewhere: RCSB PDB 4GJP · PDBe 4GJP · UniProt Q3ZD72
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