Research workbench
Rhamnogalacturonan lyase from aspergillus aculeatus K150A substrate complex
Analyse Rhamnogalacturonan lyase from aspergillus aculeatus K150A substrate complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NJV
- Type
- protein
- Length
- 508 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnogalacturonase B
- EC
- 4.2.2.10
- UniProt
- Q00019
- Ligands
- GTR, RAM, CA, SO4
- Pockets
- 4 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Rhamnogalacturonase B (EC 4.2.2.10) | protein | 508 | 6% helix, 44% strand | Q00019 |
Ligands and binding sites
- GTR · beta-D-galactopyranuronic acid · ligand · 3 copies · chains A
- RAM · alpha-L-rhamnopyranose · sugar · 3 copies · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.53 | 0.77 | 32 | empty |
| 2 | 171 | 0.47 | 0.76 | 22 | empty |
| 3 | 109 | 0.35 | 0.73 | 22 | RAM, GTR |
| 4 | 55 | 0.29 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NJV · Rhamnogalacturonan lyase from Aspergillus aculeatus K150A substrate complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q00019 · AlphaFold monomer V2.0 prediction for rhamnogalacturonate lyase a (Q00019) · a predicted model of the same protein · 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 Q00019
- Elsewhere: RCSB PDB 3NJV · PDBe 3NJV · UniProt Q00019
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