Research workbench
Crystal structure of the flax-rust effector avrm
Analyse Crystal structure of the flax-rust effector avrm in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BJM
- Type
- protein
- Length
- 873 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Avrm
- UniProt
- Q2MV46
- Ligands
- CL
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Avrm | protein | 226 | 73% helix, 0% strand | Q2MV46 |
| B | Avrm | protein | 222 | 76% helix, 0% strand | Q2MV46 |
| C | Avrm | protein | 215 | 76% helix, 0% strand | Q2MV46 |
| D | Avrm | protein | 210 | 78% helix, 0% strand | Q2MV46 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 806 | 0.83 | 0.85 | 99 | empty |
| 2 | 769 | 0.76 | 0.80 | 79 | empty |
| 3 | 822 | 0.75 | 0.79 | 76 | empty |
| 4 | 73 | 0.48 | 0.83 | 12 | empty |
| 5 | 77 | 0.47 | 0.82 | 18 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2079 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2056 Ų buried · 29 hydrogen bonds · protein-protein
- A–D · 999 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 842 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 195 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4BJM · Crystal structure of the flax-rust effector avrM · 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 Q2MV46
- Elsewhere: RCSB PDB 4BJM · PDBe 4BJM · UniProt Q2MV46
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