Research workbench
Complex of rice blast (magnaporthe oryzae) effector protein avr-pikd with the hma domain of pikp-1 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
- 6G10
- Type
- protein
- Length
- 230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Resistance protein pikp-1; Avr-pik protein
- UniProt
- E9KPB5, C4B8B8
- Ligands
- CL
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Resistance protein pikp-1 | protein | 71 | 30% helix, 37% strand | E9KPB5 |
| B | Resistance protein pikp-1 | protein | 76 | 28% helix, 37% strand | E9KPB5 |
| C | Avr-pik protein | protein | 83 | 4% helix, 46% strand | C4B8B8 |
Ligands and binding sites
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.57 | 0.84 | 27 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1053 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 495 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 116 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6G10 · 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 0.97
- 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 0.97
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 E9KPB5
- Every structure of UniProt C4B8B8
- Elsewhere: RCSB PDB 6G10 · PDBe 6G10 · UniProt E9KPB5 · UniProt C4B8B8
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