MolNFT v1 · #115786 · protein
Crystal structure of dmsp lyase dddq from ruegeria pomeroyi dss-3
5CU1: “Crystal structure of dmsp lyase dddq from ruegeria pomeroyi dss-3”. X-ray diffraction, 1 ligand (FE), 2 pockets (best druggability 0.70). MolNFT v1 #115786 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5CU1
- Type
- protein
- Length
- 197 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dmsp lyase
- UniProt
- Q5LT18
- Ligands
- FE
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dmsp lyase | protein | 197 | 22% helix, 30% strand | Q5LT18 |
Ligands and binding sites
- FE · Fe (III) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.70 | 0.97 | 16 | FE |
| 2 | 55 | 0.30 | 0.76 | 23 | empty |
Compared structures
- 5CU1 · Crystal structure of DMSP lyase DddQ from Ruegeria pomeroyi DSS-3 · the same entry in another collection · chain A against A, TM-score 1.00
- Q5LT18 · AlphaFold monomer V2.0 prediction for dimethylsulfonioproprionate lyase dddq (Q5LT18) · a predicted model of the same protein · chain A 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 Q5LT18
- Elsewhere: RCSB PDB 5CU1 · PDBe 5CU1 · UniProt Q5LT18
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