MolNFT v1 · #78224 · protein
Crystal structure of dipeptidase from streptomyces coelicolor complexed with phosphinate pseudodipeptide L-tyr-D-asp
3S2N: “Crystal structure of dipeptidase from streptomyces coelicolor complexed with phosphinate pseudodipeptide…”. X-ray diffraction, 2 ligands (P4D, ZN), 2 pockets (best druggability 0.61). MolNFT v1 #78224 on GenesisL1: 3D structure…
- PDB
- 3S2N
- Type
- protein
- Length
- 393 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- Q93J45
- Ligands
- P4D, ZN
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidase | protein | 393 | 51% helix, 12% strand | Q93J45 |
Ligands and binding sites
- P4D · (2R)-2-{[(S)-[(1R)-1-amino-2-(4-hydroxyphenyl)ethyl](hydroxy)phosphoryl]methyl}butanedioic acid · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 7 copies · 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 | 435 | 0.61 | 0.76 | 45 | P4D, ZN |
| 2 | 104 | 0.43 | 0.78 | 19 | empty |
Compared structures
- 3S2N · Crystal structure of dipeptidase from Streptomyces coelicolor complexed with phosphinate… · 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 Q93J45
- Elsewhere: RCSB PDB 3S2N · PDBe 3S2N · UniProt Q93J45
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.