Research workbench
Crystal structure of the dimethylsulfoniopropionate (dmsp) lyase dddk complexed with nickel and diacrylate
Analyse Crystal structure of the dimethylsulfoniopropionate (dmsp) lyase dddk complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TFZ
- Type
- protein
- Length
- 258 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethylsulfoniopropionate lyase dddk
- UniProt
- Q4FNM4
- Ligands
- 7BC, NI
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethylsulfoniopropionate lyase dddk | protein | 127 | 9% helix, 48% strand | Q4FNM4 |
| B | Dimethylsulfoniopropionate lyase dddk | protein | 131 | 8% helix, 47% strand | Q4FNM4 |
Ligands and binding sites
- 7BC · 3-(acryloyloxy)propanoic acid · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.65 | 0.90 | 15 | NI, 7BC |
| 2 | 82 | 0.64 | 0.90 | 18 | 7BC |
| 3 | 108 | 0.41 | 0.76 | 23 | PEG |
Interfaces
1 interface between chains.
- A–B · 1604 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5TFZ · Crystal structure of the dimethylsulfoniopropionate (DMSP) lyase DddK complexed 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 Q4FNM4
- Elsewhere: RCSB PDB 5TFZ · PDBe 5TFZ · UniProt Q4FNM4
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