Research workbench
Crystal structure of maleylpyruvate hydrolase from SPHINGOBIUM.SP syk- 6
Analyse Crystal structure of maleylpyruvate hydrolase from SPHINGOBIUM.SP syk- 6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JVV
- Type
- protein
- Length
- 525 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maleylpyruvate hydrolase
- UniProt
- G2IPX5
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maleylpyruvate hydrolase | protein | 259 | 24% helix, 38% strand | G2IPX5 |
| B | Maleylpyruvate hydrolase | protein | 266 | 23% helix, 37% strand | G2IPX5 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains B
- GOL · Glycerol · additive · 9 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.46 | 0.74 | 23 | empty |
| 2 | 186 | 0.44 | 0.74 | 23 | GOL |
| 3 | 171 | 0.43 | 0.74 | 23 | empty |
| 4 | 89 | 0.34 | 0.74 | 15 | empty |
| 5 | 57 | 0.28 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1486 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6JVV · Crystal structure of maleylpyruvate hydrolase from Sphingobium.sp SYK-6 · 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 G2IPX5
- Elsewhere: RCSB PDB 6JVV · PDBe 6JVV · UniProt G2IPX5
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