Research workbench
C9A mutant of C69-family cysteine dipeptidase from lactobacillus farciminis
Analyse C9A mutant of C69-family cysteine dipeptidase from lactobacillus farciminis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5IMG
- Type
- protein
- Length
- 4,670 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- A0A0R1IQH8
- Ligands
- CO
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J | Dipeptidase | protein | 467 | 34% helix, 20% strand | A0A0R1IQH8 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 11 copies · chains C, D, E, F, G, H, I, J
- GOL · Glycerol · additive · 6 copies · chains C, B, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.84 | 0.86 | 94 | empty |
| 2 | 1003 | 0.84 | 0.85 | 91 | empty |
| 3 | 979 | 0.84 | 0.85 | 86 | empty |
| 4 | 921 | 0.84 | 0.85 | 83 | empty |
| 5 | 940 | 0.84 | 0.85 | 85 | empty |
Interfaces
10 interfaces between chains.
- F–J · 898 Ų buried · 6 hydrogen bonds · protein-protein
- D–E · 891 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 880 Ų buried · 6 hydrogen bonds · protein-protein
- H–I · 878 Ų buried · 6 hydrogen bonds · protein-protein
- H–J · 874 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5IMG · C9A mutant of C69-family cysteine dipeptidase from Lactobacillus farciminis · 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 A0A0R1IQH8
- Elsewhere: RCSB PDB 5IMG · PDBe 5IMG · UniProt A0A0R1IQH8
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