Research workbench
Tir-dsdna complex, the initial binding state
Analyse Tir-dsdna complex, the initial binding state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7X5L
- Type
- protein + DNA
- Length
- 693 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*AP*TP*AP*AP*AP*TP*TP*A)-3'); DNA (5'-D(*TP*TP*AP*AP*TP*TP*AP*A)-3'); Flax rust…
- UniProt
- Q9XEH4
- Pockets
- 10 · best druggability 0.72
Structure
electron microscopy · 4 distinct chains · 37% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*AP*TP*AP*AP*AP*TP*TP*A)-3') | dna | 7 | — | — |
| C | DNA (5'-D(*TP*TP*AP*AP*TP*TP*AP*A)-3') | dna | 7 | — | — |
| B, E, F | Flax rust resistance protein | protein | 170 | 34% helix, 3% strand | Q9XEH4 |
| D | Flax rust resistance protein | protein | 169 | 40% helix, 2% strand | Q9XEH4 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.72 | 0.88 | 31 | empty |
| 2 | 67 | 0.71 | 0.96 | 22 | empty |
| 3 | 656 | 0.70 | 0.78 | 60 | empty |
| 4 | 95 | 0.70 | 0.92 | 25 | empty |
| 5 | 64 | 0.69 | 0.95 | 21 | empty |
Interfaces
9 interfaces between chains.
- C–B · 342 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–F · 313 Ų buried · 5 hydrogen bonds · protein-nucleic
- A–C · 263 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- C–E · 216 Ų buried · 3 hydrogen bonds · protein-nucleic
- A–B · 212 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 7X5L · Tir-dsDNA complex, the initial binding state · 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 Q9XEH4
- Elsewhere: RCSB PDB 7X5L · PDBe 7X5L · UniProt Q9XEH4
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