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A secreted lysm effector of the wheat pathogen zymoseptoria tritici protects the fungal hyphae against chitinase hydrolysis through ligand-dependent polymerisation of lysm homodimers
Analyse A secreted lysm effector of the wheat pathogen zymoseptoria tritici protects… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q40
- Type
- protein
- Length
- 315 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysm domain-containing protein
- UniProt
- F9XHX3
- Ligands
- NAG, CL
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 19% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lysm domain-containing protein | protein | 79 | 19% helix, 16% strand | F9XHX3 |
| D | Lysm domain-containing protein | protein | 78 | 19% helix, 17% strand | F9XHX3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 384 | 0.60 | 0.77 | 48 | CL |
| 2 | 126 | 0.43 | 0.76 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1181 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 1153 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 265 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 142 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 137 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6Q40 · A secreted LysM effector of the wheat pathogen Zymoseptoria tritici protects the fungal… · 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 F9XHX3
- Elsewhere: RCSB PDB 6Q40 · PDBe 6Q40 · UniProt F9XHX3
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