Research workbench
Crystal structure of the S505E mutant of tal effector DHAX3
Analyse Crystal structure of the S505E mutant of tal effector DHAX3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OSW
- Type
- protein + DNA
- Length
- 1,046 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*TP*AP*TP*CP*TP*CP*TP*CP*T)-3'); DNA (5'…
- UniProt
- Q3ZD72
- Ligands
- MG
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 73% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | HAX3 | protein | 491 | 75% helix, 0% strand | Q3ZD72 |
| B | HAX3 | protein | 487 | 72% helix, 0% strand | Q3ZD72 |
| G, I | DNA (5'- D(*TP*GP*TP*CP*CP*CP*TP*TP*TP*AP*TP*CP*TP*CP*TP*CP*T)-3') | dna | 17 | — | — |
| H, J | DNA (5'- D(*AP*GP*AP*GP*AP*GP*AP*TP*AP*AP*AP*GP*GP*GP*AP*CP*A)-3') | dna | 17 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 849 | 0.82 | 0.85 | 97 | MG |
| 2 | 921 | 0.79 | 0.82 | 108 | empty |
| 3 | 240 | 0.57 | 0.78 | 31 | empty |
| 4 | 136 | 0.35 | 0.72 | 17 | empty |
| 5 | 54 | 0.33 | 0.77 | 14 | empty |
Interfaces
9 interfaces between chains.
- B–G · 1725 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–I · 1716 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 764 Ų buried · 5 hydrogen bonds · protein-protein
- I–J · 758 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- G–H · 745 Ų buried · 72 hydrogen bonds · nucleic-nucleic
Compared structures
- 4OSW · Crystal structure of the S505E mutant of TAL effector dHax3 · 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 4OSW · PDBe 4OSW · UniProt Q3ZD72
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