MolNFT v1 · #153958 · protein
Crystal structure of maleylpyruvate hydrolase from sphingobium sp. syk-6 in complex with manganese (II) ion and pyruvate
6JVW: “Crystal structure of maleylpyruvate hydrolase from sphingobium sp. syk-6 in complex with manganese (II) ion…”. X-ray diffraction, 2 ligands (PYR, MN), 5 pockets (best druggability 0.52). MolNFT v1 #153958 on GenesisL1: 3D structure…
- PDB
- 6JVW
- Type
- protein
- Length
- 524 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maleylpyruvate hydrolase
- UniProt
- G2IPX5
- Ligands
- PYR, MN
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maleylpyruvate hydrolase | protein | 260 | 23% helix, 37% strand | G2IPX5 |
| B | Maleylpyruvate hydrolase | protein | 264 | 23% helix, 37% strand | G2IPX5 |
Ligands and binding sites
- PYR · Pyruvic acid · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 283 | 0.52 | 0.74 | 42 | PYR, MN |
| 2 | 194 | 0.46 | 0.74 | 28 | empty |
| 3 | 172 | 0.43 | 0.74 | 23 | empty |
| 4 | 61 | 0.32 | 0.76 | 16 | empty |
| 5 | 58 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1479 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6JVW · Crystal structure of maleylpyruvate hydrolase from Sphingobium sp. SYK-6 in complex with… · 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 6JVW · PDBe 6JVW · UniProt G2IPX5
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