Research workbench
Rhamnogalacturonan lyase from aspergillus aculeatus K150A active site mutant
Analyse Rhamnogalacturonan lyase from aspergillus aculeatus K150A active site mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XHN
- Type
- protein
- Length
- 1,016 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rhamnogalacturonase B
- EC
- 4.2.2.10
- UniProt
- Q00019
- Ligands
- CA, SO4
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rhamnogalacturonase B (EC 4.2.2.10) | protein | 508 | 7% helix, 44% strand | Q00019 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 970 | 0.81 | 0.82 | 87 | empty |
| 2 | 356 | 0.57 | 0.76 | 40 | empty |
| 3 | 222 | 0.53 | 0.77 | 31 | empty |
| 4 | 202 | 0.53 | 0.78 | 30 | empty |
| 5 | 184 | 0.50 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 726 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2XHN · Rhamnogalacturonan lyase from Aspergillus aculeatus K150A active site mutant · 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 2XHN · PDBe 2XHN · UniProt Q00019
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