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The crystal structure of the dipeptidase ac, metallo peptidase. merops family M19
Analyse The crystal structure of the dipeptidase ac, metallo peptidase. merops family… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FDG
- Type
- protein
- Length
- 686 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase ac. metallo peptidase. merops family M19
- UniProt
- Q3IZQ3
- Ligands
- MG
- Pockets
- 5 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dipeptidase ac. metallo peptidase. merops family M19 | protein | 338 | 44% helix, 15% strand | Q3IZQ3 |
| B | Dipeptidase ac. metallo peptidase. merops family M19 | protein | 348 | 44% helix, 15% strand | Q3IZQ3 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 381 | 0.68 | 0.81 | 43 | empty |
| 2 | 174 | 0.49 | 0.77 | 27 | empty |
| 3 | 122 | 0.43 | 0.77 | 29 | empty |
| 4 | 94 | 0.36 | 0.75 | 16 | empty |
| 5 | 73 | 0.32 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3FDG · The crystal structure of the dipeptidase AC, Metallo peptidase. MEROPS family M19 · 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 Q3IZQ3
- Elsewhere: RCSB PDB 3FDG · PDBe 3FDG · UniProt Q3IZQ3
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