Research workbench
Crystal structure of human tdp-43 RRM1 domain with D169G mutation in complex with an unmodified single-stranded DNA
Analyse Crystal structure of human tdp-43 RRM1 domain with D169G mutation in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4Y00
- Type
- protein + DNA
- Length
- 334 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tar DNA-binding protein 43; DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3')
- UniProt
- Q13148
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Tar DNA-binding protein 43 | protein | 78 | 21% helix, 40% strand | Q13148 |
| C, D | Tar DNA-binding protein 43 | protein | 77 | 19% helix, 40% strand | Q13148 |
| E | DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3') | dna | 8 | — | — |
| F | DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3') | dna | 9 | — | — |
| G | DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3') | dna | 4 | — | — |
| H | DNA (5'-D(P*TP*TP*GP*AP*GP*CP*GP*T)-3') | dna | 3 | — | — |
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.64 | 0.75 | 49 | empty |
| 2 | 127 | 0.61 | 0.86 | 22 | empty |
| 3 | 226 | 0.49 | 0.75 | 35 | empty |
Interfaces
11 interfaces between chains.
- A–E · 735 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–F · 719 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–G · 544 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–H · 392 Ų buried · 9 hydrogen bonds · protein-nucleic
- C–D · 282 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4Y00 · Crystal Structure of Human TDP-43 RRM1 Domain with D169G Mutation in Complex with an… · the same entry in another collection · chain H against H, TM-score 1.00
- Q13148 · AlphaFold monomer V2.0 prediction for tar DNA-binding protein 43 (Q13148) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 Q13148
- Elsewhere: RCSB PDB 4Y00 · PDBe 4Y00 · UniProt Q13148
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