Research workbench
Crystal structure of the E100A mutant tir domain from the grapevine disease resistance protein RUN1 bound to NAD
Analyse Crystal structure of the E100A mutant tir domain from the grapevine disease… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7S2Z
- Type
- protein
- Length
- 684 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disease resistance protein RUN1
- EC
- 3.2.2.6, 3.2.2.-
- UniProt
- V9M398
- Ligands
- NAD, SO4
- Pockets
- 10 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Disease resistance protein RUN1 (EC 3.2.2.6, 3.2.2.-) | protein | 171 | 52% helix, 15% strand | V9M398 |
| B | Disease resistance protein RUN1 (EC 3.2.2.6, 3.2.2.-) | protein | 173 | 53% helix, 14% strand | V9M398 |
| C, D | Disease resistance protein RUN1 (EC 3.2.2.6, 3.2.2.-) | protein | 170 | 49% helix, 16% strand | V9M398 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 18 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.69 | 0.84 | 26 | SO4 |
| 2 | 198 | 0.67 | 0.85 | 23 | SO4 |
| 3 | 176 | 0.61 | 0.83 | 21 | SO4 |
| 4 | 179 | 0.59 | 0.81 | 21 | SO4 |
| 5 | 267 | 0.53 | 0.75 | 34 | empty |
Interfaces
5 interfaces between chains.
- B–D · 712 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 706 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 367 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 343 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7S2Z · Crystal structure of the E100A mutant TIR domain from the grapevine disease resistance… · the same entry in another collection · chain A against A, TM-score 1.00
- V9M398 · AlphaFold monomer V2.0 prediction for disease resistance protein RUN1 (V9M398) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 V9M398
- Elsewhere: RCSB PDB 7S2Z · PDBe 7S2Z · UniProt V9M398
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