Research workbench
Pandda analysis group deposition -- crystal structure of porphyromonas gingivalis in complex with Z2856434912
Analyse Pandda analysis group deposition -- crystal structure of porphyromonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SDC
- Type
- protein
- Length
- 1,392 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ASP/GLU-specific dipeptidyl-peptidase
- EC
- 3.4.14.-
- UniProt
- B2RID1
- Ligands
- LDV, CL
- Pockets
- 14 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 697 | 50% helix, 16% strand | B2RID1 |
| B | ASP/GLU-specific dipeptidyl-peptidase (EC 3.4.14.-) | protein | 695 | 50% helix, 16% strand | B2RID1 |
Ligands and binding sites
- LDV · 3-[(4-methylpiperidin-1-yl)methyl]-1H-indole · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 795 | 0.71 | 0.77 | 81 | LDV |
| 2 | 769 | 0.71 | 0.77 | 79 | LDV |
| 3 | 296 | 0.51 | 0.74 | 45 | empty |
| 4 | 150 | 0.40 | 0.74 | 25 | empty |
| 5 | 82 | 0.37 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 732 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5SDC · PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in… · the same entry in another collection · chain A against A, TM-score 1.00
- B2RID1 · AlphaFold monomer V2.0 prediction for ASP/GLU-specific dipeptidyl- peptidase (B2RID1) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 B2RID1
- Elsewhere: RCSB PDB 5SDC · PDBe 5SDC · UniProt B2RID1
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