Research workbench
Crystal structure of the RPS4 and RRS1 tir domain heterodimer
Analyse Crystal structure of the RPS4 and RRS1 tir domain heterodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4C6T
- Type
- protein
- Length
- 613 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable wrky transcription factor 52; Disease resistance protein RPS4
- UniProt
- Q9FH83, Q9XGM3
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable wrky transcription factor 52 | protein | 141 | 45% helix, 19% strand | Q9FH83 |
| B | Disease resistance protein RPS4 | protein | 166 | 55% helix, 15% strand | Q9XGM3 |
| C | Probable wrky transcription factor 52 | protein | 143 | 47% helix, 20% strand | Q9FH83 |
| D | Disease resistance protein RPS4 | protein | 163 | 56% helix, 15% strand | Q9XGM3 |
Ligands and binding sites
- MLA · Malonic acid · additive · 2 copies · chains A, C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 294 | 0.71 | 0.85 | 36 | MLA |
| 2 | 441 | 0.71 | 0.82 | 49 | empty |
| 3 | 325 | 0.71 | 0.84 | 37 | MLA |
| 4 | 161 | 0.46 | 0.76 | 40 | empty |
| 5 | 69 | 0.45 | 0.83 | 15 | empty |
Interfaces
5 interfaces between chains.
- A–B · 760 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 665 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 546 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 524 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 512 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4C6T · Crystal structure of the RPS4 and RRS1 TIR domain heterodimer · the same entry in another collection · chain A against A, TM-score 1.00
- Q9XGM3 · AlphaFold monomer V2.0 prediction for disease resistance protein RPS4 (Q9XGM3) · a predicted model of the same protein · chain D against A, TM-score 0.93
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 Q9FH83
- Every structure of UniProt Q9XGM3
- Elsewhere: RCSB PDB 4C6T · PDBe 4C6T · UniProt Q9FH83 · UniProt Q9XGM3
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