Research workbench
Crystal structure of the E.COLI dipeptidyl carboxypeptidase dcp in complex with a peptidic inhibitor
Analyse Crystal structure of the E.COLI dipeptidyl carboxypeptidase dcp in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y79
- Type
- protein
- Length
- 684 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptidyl-dipeptidase dcp
- EC
- 3.4.15.5
- UniProt
- P24171
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 58% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | Peptidyl-dipeptidase dcp (EC 3.4.15.5) | protein | 684 | 58% helix, 7% strand | P24171 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains 1
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.86 | 0.87 | 99 | empty |
| 2 | 435 | 0.76 | 0.85 | 55 | empty |
| 3 | 340 | 0.75 | 0.86 | 40 | empty |
| 4 | 309 | 0.69 | 0.83 | 27 | empty |
| 5 | 59 | 0.44 | 0.83 | 15 | empty |
Compared structures
- 1Y79 · Crystal Structure of the E.coli Dipeptidyl Carboxypeptidase Dcp in Complex with a… · the same entry in another collection · chain 1 against 1, TM-score 1.00
- P24171 · AlphaFold monomer V2.0 prediction for dipeptidyl carboxypeptidase (P24171) · a predicted model of the same protein · chain 1 against A, TM-score 0.99
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 P24171
- Elsewhere: RCSB PDB 1Y79 · PDBe 1Y79 · UniProt P24171
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