Research workbench
Crystal structure of the tir domain from the muscadinia rotundifolia disease resistance protein RPV1
Analyse Crystal structure of the tir domain from the muscadinia rotundifolia disease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KU7
- Type
- protein
- Length
- 338 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tir-nb-lrr type resistance protein RPV1
- UniProt
- V9M2S5
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tir-nb-lrr type resistance protein RPV1 | protein | 171 | 54% helix, 16% strand | V9M2S5 |
| B | Tir-nb-lrr type resistance protein RPV1 | protein | 167 | 52% helix, 16% strand | V9M2S5 |
Ligands and binding sites
- MLA · Malonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.51 | 0.80 | 18 | MLA |
| 2 | 96 | 0.48 | 0.81 | 24 | empty |
| 3 | 125 | 0.48 | 0.79 | 18 | MLA |
| 4 | 99 | 0.35 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 721 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5KU7 · Crystal structure of the TIR domain from the Muscadinia rotundifolia disease resistance… · the same entry in another collection · chain A against A, TM-score 1.00
- V9M2S5 · AlphaFold monomer V2.0 prediction for disease resistance protein RPV1 (V9M2S5) · a predicted model of the same protein · chain B 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 V9M2S5
- Elsewhere: RCSB PDB 5KU7 · PDBe 5KU7 · UniProt V9M2S5
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