MolNFT v1 · #153806 · protein
Crystal structure of phyllogen, a phyllody inducing effector protein of phytoplasma.
6JQA · Phytoplasmal effector causing phyllody 1: “Crystal structure of phyllogen, a phyllody inducing effector protein of phytoplasma.”. X-ray diffraction, 1 ligand (IOD), 4 pockets (best druggability 0.86). MolNFT v1 #153806 on GenesisL1…
- PDB
- 6JQA
- Type
- protein
- Length
- 335 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phytoplasmal effector causing phyllody 1
- UniProt
- X5IFG3
- Ligands
- IOD
- Pockets
- 4 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phytoplasmal effector causing phyllody 1 | protein | 85 | 75% helix, 0% strand | X5IFG3 |
| B | Phytoplasmal effector causing phyllody 1 | protein | 88 | 73% helix, 0% strand | X5IFG3 |
| C | Phytoplasmal effector causing phyllody 1 | protein | 81 | 73% helix, 0% strand | X5IFG3 |
| D | Phytoplasmal effector causing phyllody 1 | protein | 81 | 79% helix, 0% strand | X5IFG3 |
Ligands and binding sites
- IOD · Iodide ion · ion · 19 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 566 | 0.86 | 0.91 | 67 | empty |
| 2 | 237 | 0.64 | 0.82 | 29 | empty |
| 3 | 124 | 0.47 | 0.79 | 19 | empty |
| 4 | 70 | 0.34 | 0.76 | 17 | IOD |
Interfaces
6 interfaces between chains.
- A–B · 1181 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1143 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 960 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 695 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 505 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 modified (nonstandard).
Compared structures
- 6JQA · Crystal structure of phyllogen, a phyllody inducing effector protein of phytoplasma. · 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 X5IFG3
- Elsewhere: RCSB PDB 6JQA · PDBe 6JQA · UniProt X5IFG3
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