Research workbench
Crystal structure of pseudomonas aeruginosa opdk with vanillate
Analyse Crystal structure of pseudomonas aeruginosa opdk with vanillate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Y2X
- Type
- protein
- Length
- 752 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vanillate porin opdk
- UniProt
- Q9HUR5
- Ligands
- VNL
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 64% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vanillate porin opdk | protein | 374 | 1% helix, 64% strand | Q9HUR5 |
| B | Vanillate porin opdk | protein | 378 | 1% helix, 63% strand | Q9HUR5 |
Ligands and binding sites
- VNL · 4-hydroxy-3-methoxybenzoate · ligand · 4 copies · chains A, B
- C8E · (hydroxyethyloxy)tri(ethyloxy)octane · additive · 29 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 952 | 0.72 | 0.76 | 94 | empty |
| 2 | 924 | 0.71 | 0.76 | 96 | EDO |
| 3 | 210 | 0.52 | 0.77 | 27 | VNL |
| 4 | 207 | 0.51 | 0.77 | 29 | VNL |
| 5 | 77 | 0.30 | 0.73 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 338 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 2Y2X · Crystal Structure of Pseudomonas Aeruginosa OpdK with Vanillate · 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 Q9HUR5
- Elsewhere: RCSB PDB 2Y2X · PDBe 2Y2X · UniProt Q9HUR5
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