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Crystal structure of oligogalacturonate lyase (VPA0088) from vibrio parahaemolyticus. northeast structural genomics consortium target VPR199
Analyse Crystal structure of oligogalacturonate lyase (VPA0088) from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C5M
- Type
- protein
- Length
- 1,130 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligogalacturonate lyase
- UniProt
- Q87K10
- Ligands
- MN
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Oligogalacturonate lyase | protein | 376 | 3% helix, 45% strand | Q87K10 |
| B | Oligogalacturonate lyase | protein | 378 | 3% helix, 45% strand | Q87K10 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 956 | 0.81 | 0.83 | 84 | empty |
| 2 | 464 | 0.79 | 0.87 | 38 | empty |
| 3 | 459 | 0.79 | 0.86 | 39 | empty |
| 4 | 820 | 0.73 | 0.78 | 78 | empty |
| 5 | 625 | 0.72 | 0.79 | 66 | empty |
Interfaces
2 interfaces between chains.
- A–B · 573 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 515 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3C5M · Crystal structure of oligogalacturonate lyase (VPA0088) from Vibrio parahaemolyticus.… · 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 Q87K10
- Elsewhere: RCSB PDB 3C5M · PDBe 3C5M · UniProt Q87K10
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