Research workbench
Crystal structure of dimethylsulphoniopropionate (dmsp) lyase dddq
Analyse Crystal structure of dimethylsulphoniopropionate (dmsp) lyase dddq in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4LA2
- Type
- protein
- Length
- 382 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dimethylsulphoniopropionate (dmsp) lyase dddq
- UniProt
- D0CY60
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dimethylsulphoniopropionate (dmsp) lyase dddq | protein | 190 | 23% helix, 35% strand | D0CY60 |
| B | Dimethylsulphoniopropionate (dmsp) lyase dddq | protein | 192 | 24% helix, 35% strand | D0CY60 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.75 | 0.95 | 21 | ZN, MES |
| 2 | 390 | 0.74 | 0.84 | 63 | MES |
Interfaces
1 interface between chains.
- A–B · 510 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4LA2 · Crystal structure of dimethylsulphoniopropionate (DMSP) lyase DddQ · the same entry in another collection · chain A against A, TM-score 1.00
- D0CY60 · AlphaFold monomer V2.0 prediction for dimethylsulfonioproprionate lyase dddq (D0CY60) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 D0CY60
- Elsewhere: RCSB PDB 4LA2 · PDBe 4LA2 · UniProt D0CY60
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