Research workbench
Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2- pyrrolidone
Analyse Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2- pyrrolidone in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PLD
- Type
- protein
- Length
- 576 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smp-30/CGR1 family protein
- EC
- 3.1.1.68
- UniProt
- Q9A9Z1
- Ligands
- 7UK, FE2
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smp-30/CGR1 family protein (EC 3.1.1.68) | protein | 287 | 3% helix, 55% strand | Q9A9Z1 |
| B | Smp-30/CGR1 family protein (EC 3.1.1.68) | protein | 289 | 3% helix, 54% strand | Q9A9Z1 |
Ligands and binding sites
- 7UK · (R)-4-hydroxy-2-pyrrolidone · ligand · 5 copies · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 132 | 0.77 | 0.95 | 25 | empty |
| 2 | 137 | 0.76 | 0.94 | 29 | empty |
| 3 | 440 | 0.74 | 0.83 | 62 | empty |
| 4 | 97 | 0.64 | 0.89 | 17 | 7UK |
| 5 | 86 | 0.60 | 0.88 | 16 | 7UK |
Interfaces
1 interface between chains.
- A–B · 454 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7PLD · Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone · 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 Q9A9Z1
- Elsewhere: RCSB PDB 7PLD · PDBe 7PLD · UniProt Q9A9Z1
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