Research workbench
Avirulence protein 4 (AVR4) from cladosporium fulvum bound to the hexasaccharide of chitin
Analyse Avirulence protein 4 (AVR4) from cladosporium fulvum bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BN0
- Type
- protein
- Length
- 311 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Race-specific elicitor A4
- UniProt
- Q00363
- Ligands
- NAG, CL
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 13% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Race-specific elicitor A4 | protein | 79 | 13% helix, 29% strand | Q00363 |
| B | Race-specific elicitor A4 | protein | 77 | 13% helix, 35% strand | Q00363 |
| D | Race-specific elicitor A4 | protein | 76 | 13% helix, 30% strand | Q00363 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 24 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.56 | 0.73 | 42 | NAG |
| 2 | 385 | 0.54 | 0.73 | 40 | NAG |
| 3 | 51 | 0.37 | 0.80 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 637 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 60 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 59 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 6BN0 · Avirulence protein 4 (Avr4) from Cladosporium fulvum bound to the hexasaccharide of chitin · the same entry in another collection · chain D against D, TM-score 1.00
- Q00363 · AlphaFold monomer V2.0 prediction for race-specific elicitor A4 (Q00363) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 Q00363
- Elsewhere: RCSB PDB 6BN0 · PDBe 6BN0 · UniProt Q00363
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