Research workbench
D31P mutant of C69-family cysteine dipeptidase from lactobacillus farciminis
Analyse D31P 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
- 5IMH
- Type
- protein
- Length
- 2,335 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- A0A0R1IQH8
- Ligands
- CO
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Dipeptidase | protein | 467 | 32% helix, 19% strand | A0A0R1IQH8 |
Ligands and binding sites
- CO · Cobalt (II) ion · metal · 7 copies · chains A, B, C, D, E
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, C
- ACT · Acetate ion · additive · chains B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 876 | 0.85 | 0.87 | 87 | empty |
| 2 | 890 | 0.85 | 0.87 | 90 | empty |
| 3 | 1088 | 0.85 | 0.86 | 100 | empty |
| 4 | 1074 | 0.84 | 0.85 | 97 | empty |
| 5 | 1150 | 0.84 | 0.85 | 101 | empty |
Interfaces
5 interfaces between chains.
- D–E · 1170 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1155 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1134 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1101 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 1076 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5IMH · D31P 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 5IMH · PDBe 5IMH · UniProt A0A0R1IQH8
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