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Crystal structure of a lactonase from cladophialophora bantiana
Analyse Crystal structure of a lactonase from cladophialophora bantiana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XWZ
- Type
- protein
- Length
- 1,048 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Unplaced genomic scaffold SUPERCONT1.36, whole genome shotgun sequence
- UniProt
- A0A0D2H023
- Ligands
- NA
- Pockets
- 9 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Unplaced genomic scaffold SUPERCONT1.36, whole genome shotgun sequence | protein | 260 | 48% helix, 18% strand | A0A0D2H023 |
| B | Unplaced genomic scaffold SUPERCONT1.36, whole genome shotgun sequence | protein | 264 | 45% helix, 18% strand | A0A0D2H023 |
| C, D | Unplaced genomic scaffold SUPERCONT1.36, whole genome shotgun sequence | protein | 262 | 46% helix, 18% strand | A0A0D2H023 |
Ligands and binding sites
- NA · Sodium ion · metal · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains B, D
- MLI · Malonate ion · additive · 2 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.72 | 0.85 | 31 | GOL |
| 2 | 221 | 0.71 | 0.87 | 31 | empty |
| 3 | 249 | 0.69 | 0.84 | 34 | GOL, MLI |
| 4 | 283 | 0.65 | 0.81 | 33 | MLI |
| 5 | 123 | 0.62 | 0.87 | 19 | NA |
Interfaces
4 interfaces between chains.
- C–D · 636 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 624 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 466 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 221 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5XWZ · Crystal structure of a lactonase from Cladophialophora bantiana · 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 A0A0D2H023
- Elsewhere: RCSB PDB 5XWZ · PDBe 5XWZ · UniProt A0A0D2H023
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