MolNFT v1 · #68768 · protein
Crystal structure of dipeptidase from streptomics coelicolor complexed with phosphinate pseudodipeptide L-ala-D-asp at 1.4A resolution.
3K5X: “Crystal structure of dipeptidase from streptomics coelicolor complexed with phosphinate pseudodipeptide…”. X-ray diffraction, 2 ligands (P8D, ZN), 2 pockets (best druggability 0.60). MolNFT v1 #68768 on GenesisL1: 3D structure…
- PDB
- 3K5X
- Type
- protein
- Length
- 391 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- Q93J45
- Ligands
- P8D, ZN
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidase | protein | 391 | 51% helix, 13% strand | Q93J45 |
Ligands and binding sites
- P8D · phosphinate pseudodipeptide L-Ala-D-Asp · ligand · chains A
- ZN · Zinc ion · metal · 2 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 | 417 | 0.60 | 0.76 | 42 | P8D, ZN |
| 2 | 107 | 0.43 | 0.78 | 19 | empty |
Compared structures
- 3K5X · Crystal structure of dipeptidase from Streptomics 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 3K5X · PDBe 3K5X · UniProt Q93J45
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