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Complex of rice blast (magnaporthe oryzae) effector protein APIKL2F with the host target SHMA94 from setaria italica
Analyse Complex of rice blast (magnaporthe oryzae) effector protein APIKL2F with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NMM
- Type
- protein
- Length
- 1,350 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Shmax; APIKL2F
- UniProt
- K3YDQ6
- Ligands
- CL
- Pockets
- 19 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E, F, G, H | Shmax | protein | 78 | 31% helix, 36% strand | K3YDQ6 |
| C | Shmax | protein | 77 | 31% helix, 39% strand | K3YDQ6 |
| I, J, K, M, N, O, P | APIKL2F | protein | 91 | 11% helix, 42% strand | — |
| L | APIKL2F | protein | 90 | 10% helix, 42% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains M
- EDO · 1,2-ethanediol · additive · 13 copies · chains C, K, L, E, N, I, A, J, D, M, P
- 1PE · Pentaethylene glycol · additive · 2 copies · chains F, L, N, H, P
- PEG · Di(hydroxyethyl)ether · additive · chains O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.83 | 0.86 | 81 | empty |
| 2 | 542 | 0.76 | 0.83 | 72 | empty |
| 3 | 221 | 0.76 | 0.90 | 26 | empty |
| 4 | 384 | 0.62 | 0.77 | 27 | empty |
| 5 | 156 | 0.61 | 0.83 | 29 | empty |
Interfaces
33 interfaces between chains.
- H–P · 1047 Ų buried · 21 hydrogen bonds · protein-protein
- F–N · 1042 Ų buried · 20 hydrogen bonds · protein-protein
- D–L · 1037 Ų buried · 22 hydrogen bonds · protein-protein
- A–I · 1035 Ų buried · 24 hydrogen bonds · protein-protein
- G–O · 1029 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7NMM · Complex of rice blast (Magnaporthe oryzae) effector protein APikL2F with the host target… · 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 K3YDQ6
- Elsewhere: RCSB PDB 7NMM · PDBe 7NMM · UniProt K3YDQ6
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