Research workbench
A C69-family cysteine dipeptidase in complex with ala-pro from lactobacillus farciminis
Analyse A C69-family cysteine dipeptidase in complex with ala-pro from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5INR
- Type
- protein
- Length
- 2,315 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dipeptidase
- UniProt
- A0A0R1IQH8
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Dipeptidase | protein | 463 | 35% helix, 19% strand | A0A0R1IQH8 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 35 copies · chains A, B, E, D, C
- ACT · Acetate ion · additive · chains 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.81 | 0.82 | 85 | EDO |
| 2 | 1111 | 0.81 | 0.82 | 84 | EDO |
| 3 | 1139 | 0.81 | 0.82 | 84 | EDO |
| 4 | 1171 | 0.81 | 0.82 | 85 | EDO |
| 5 | 1158 | 0.81 | 0.82 | 86 | EDO |
Interfaces
5 interfaces between chains.
- A–B · 887 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 883 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 882 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 851 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5INR · A C69-family cysteine dipeptidase in complex with Ala-Pro 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 5INR · PDBe 5INR · UniProt A0A0R1IQH8
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