Research workbench
Crystal structure of a pl 26 exo-rhamnogalacturonan lyase from penicillium chrysogenum complexed with tetrameric substrate
Analyse Crystal structure of a pl 26 exo-rhamnogalacturonan lyase from penicillium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XQO
- Type
- protein
- Length
- 1,780 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcrglx protein
- UniProt
- A0A0C6EFY4
- Ligands
- GAD, RAM, ADA, CA
- Pockets
- 19 · best druggability 0.91
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pcrglx protein | protein | 899 | 30% helix, 26% strand | A0A0C6EFY4 |
| B | Pcrglx protein | protein | 881 | 30% helix, 26% strand | A0A0C6EFY4 |
Ligands and binding sites
- GAD · 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid · ligand · 2 copies · chains A, B
- RAM · alpha-L-rhamnopyranose · sugar · 4 copies · chains A, B
- ADA · alpha-D-galactopyranuronic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1032 | 0.91 | 0.93 | 130 | empty |
| 2 | 135 | 0.80 | 0.97 | 31 | empty |
| 3 | 124 | 0.78 | 0.97 | 25 | empty |
| 4 | 68 | 0.74 | 0.98 | 18 | empty |
| 5 | 54 | 0.71 | 0.98 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 5153 Ų buried · 102 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 2 disulfide, 2 glycan (engineered, disulfide, glycosylation).
Compared structures
- 5XQO · Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum… · 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 A0A0C6EFY4
- Elsewhere: RCSB PDB 5XQO · PDBe 5XQO · UniProt A0A0C6EFY4
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