Research workbench
Crystal structure of a pl 26 exo-rhamnogalacturonan lyase from penicillium chrysogenum complexed with unsaturated galacturonosyl rhamnose substituted with galactose
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
- 5XQJ
- Type
- protein
- Length
- 7,135 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pcrglx protein
- UniProt
- A0A0C6EFY4
- Ligands
- GAD, RAM, GAL, CA
- Pockets
- 20 · best druggability 0.91
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pcrglx protein | protein | 896 | 30% helix, 26% strand | A0A0C6EFY4 |
| C | Pcrglx protein | protein | 885 | 30% helix, 26% strand | A0A0C6EFY4 |
| D | Pcrglx protein | protein | 884 | 30% helix, 26% strand | A0A0C6EFY4 |
| E | Pcrglx protein | protein | 900 | 31% helix, 26% strand | A0A0C6EFY4 |
| F | Pcrglx protein | protein | 900 | 30% helix, 26% strand | A0A0C6EFY4 |
| G | Pcrglx protein | protein | 886 | 30% helix, 26% strand | A0A0C6EFY4 |
| H | Pcrglx protein | protein | 888 | 30% helix, 26% strand | A0A0C6EFY4 |
Ligands and binding sites
- GAD · 2,6-anhydro-3-deoxy-L-threo-hex-2-enonic acid · ligand · 8 copies · chains A, B, C, D, E, H, F, G
- RAM · alpha-L-rhamnopyranose · sugar · 8 copies · chains A, B, C, D, E, F, G, H
- GAL · beta-D-galactopyranose · sugar · 5 copies · chains A, C, E, F, G
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.91 | 0.94 | 135 | empty |
| 2 | 1164 | 0.91 | 0.93 | 145 | empty |
| 3 | 826 | 0.89 | 0.92 | 105 | empty |
| 4 | 583 | 0.88 | 0.94 | 75 | empty |
| 5 | 421 | 0.86 | 0.94 | 53 | empty |
Interfaces
9 interfaces between chains.
- F–G · 5151 Ų buried · 93 hydrogen bonds · protein-protein
- E–H · 5139 Ų buried · 96 hydrogen bonds · protein-protein
- B–C · 5134 Ų buried · 96 hydrogen bonds · protein-protein
- A–D · 5127 Ų buried · 93 hydrogen bonds · protein-protein
- B–E · 724 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, glycosylation).
Compared structures
- 5XQJ · 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 5XQJ · PDBe 5XQJ · UniProt A0A0C6EFY4
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