MolNFT v1 · #162423 · protein
Complex of rice blast (magnaporthe oryzae) effector protein avr-pike with an engineered hma domain of pikp-1 from rice (oryza sativa)
6R8M · Nbs-lrr class disease resistance protein pikh-1: “Complex of rice blast (magnaporthe oryzae) effector protein avr-pike with an engineered hma domain of pikp-1…”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.60).…
- PDB
- 6R8M
- Type
- protein
- Length
- 467 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nbs-lrr class disease resistance protein pikh-1; Avr-pik protein
- UniProt
- D5L9G5, C4B8C2
- Ligands
- CL
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 19% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nbs-lrr class disease resistance protein pikh-1 | protein | 74 | 28% helix, 41% strand | D5L9G5 |
| B | Nbs-lrr class disease resistance protein pikh-1 | protein | 78 | 26% helix, 36% strand | D5L9G5 |
| C | Avr-pik protein | protein | 82 | 4% helix, 46% strand | C4B8C2 |
| E | Nbs-lrr class disease resistance protein pikh-1 | protein | 73 | 29% helix, 37% strand | D5L9G5 |
| F | Nbs-lrr class disease resistance protein pikh-1 | protein | 77 | 26% helix, 36% strand | D5L9G5 |
| G | Avr-pik protein | protein | 83 | 4% helix, 46% strand | C4B8C2 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains B, C, F, G
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains B, C, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.60 | 0.85 | 29 | empty |
| 2 | 62 | 0.48 | 0.85 | 17 | empty |
| 3 | 155 | 0.46 | 0.76 | 22 | empty |
| 4 | 95 | 0.44 | 0.79 | 14 | empty |
| 5 | 52 | 0.32 | 0.77 | 14 | empty |
Interfaces
9 interfaces between chains.
- B–C · 1065 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1060 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 510 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 502 Ų buried · 10 hydrogen bonds · protein-protein
- C–E · 333 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6R8M · Complex of rice blast (Magnaporthe oryzae) effector protein AVR-PikE with an engineered… · the same entry in another collection · chain A against A, TM-score 1.00
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 D5L9G5
- Every structure of UniProt C4B8C2
- Elsewhere: RCSB PDB 6R8M · PDBe 6R8M · UniProt D5L9G5 · UniProt C4B8C2
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