Research workbench
Crystal structure of POPP2 in complex with IP6, accoa and the wrky domain of RRS1-R .
Analyse Crystal structure of POPP2 in complex with IP6, accoa and the wrky domain of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5W3X
- Type
- protein
- Length
- 817 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- POPP2 protein; Disease resistance protein RRS1
- UniProt
- A0A0S4VB05, C4B7M5
- Ligands
- IHP, ACO, ZN
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | POPP2 protein | protein | 335 | 46% helix, 20% strand | A0A0S4VB05 |
| B | Disease resistance protein RRS1 | protein | 67 | 6% helix, 37% strand | C4B7M5 |
| C | POPP2 protein | protein | 342 | 46% helix, 19% strand | A0A0S4VB05 |
| D | Disease resistance protein RRS1 | protein | 73 | 5% helix, 40% strand | C4B7M5 |
Ligands and binding sites
- IHP · Inositol hexakisphosphate · ligand · 2 copies · chains A, C
- ACO · Acetyl coenzyme *A · ligand · 2 copies · chains A, C
- ZN · Zinc ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.73 | 0.80 | 80 | ACO |
| 2 | 368 | 0.69 | 0.82 | 54 | ACO |
| 3 | 214 | 0.57 | 0.80 | 36 | empty |
| 4 | 51 | 0.54 | 0.90 | 19 | empty |
| 5 | 106 | 0.54 | 0.83 | 21 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1350 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1318 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5W3X · Crystal structure of PopP2 in complex with IP6, AcCoA and the WRKY domain of RRS1-R . · the same entry in another collection · chain C against C, TM-score 1.00
- C4B7M5 · AlphaFold monomer V2.0 prediction for disease resistance protein RRS1 (C4B7M5) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 A0A0S4VB05
- Every structure of UniProt C4B7M5
- Elsewhere: RCSB PDB 5W3X · PDBe 5W3X · UniProt A0A0S4VB05 · UniProt C4B7M5
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