Research workbench
Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the HMA domain of Pikp1 from rice (Oryza sativa)
Analyse Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A6W
- Type
- protein
- Length
- 227 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- MAGNAPORTHE ORYZAE; ORYZA SATIVA
- Molecule
- Resistance protein pikp-1; Avr-pik protein
- UniProt
- E9KPB5, C4B8B8
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · resolution 1.6 · 3 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Resistance protein pikp-1 | protein | 71 | 31% helix, 37% strand | E9KPB5 |
| B | Resistance protein pikp-1 | protein | 73 | 29% helix, 36% strand | E9KPB5 |
| C | Avr-pik protein | protein | 83 | 0% helix, 46% strand | C4B8B8 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 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 | 0.58 | 0.84 | 27 | EDO |
| 2 | 62 | 0.31 | 0.75 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–C · 951 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 481 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 131 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5A6W · Complex of rice blast (magnaporthe oryzae) effector protein avr-pikd with the hma domain… · the same entry in another collection · chain A against A, TM-score 1.00
- 7BNT · Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikD with a predicted… · a predicted model of the same protein · chain C against C, TM-score 0.99
- 7BNT · Complex of rice blast (magnaporthe oryzae) effector protein avr-pikd with a predicted… · a predicted model of the same protein · chain C against C, TM-score 0.99
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 E9KPB5
- Every structure of UniProt C4B8B8
- Elsewhere: RCSB PDB 5A6W · PDBe 5A6W · UniProt E9KPB5 · UniProt C4B8B8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.