Research workbench
Crystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase
Analyse Crystal structure of carboxypeptidase Y inhibitor complexed with the cognate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WPX
- Type
- protein
- Length
- 625 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Carboxypeptidase Y; Carboxypeptidase Y inhibitor
- EC
- 3.4.16.5
- UniProt
- P00729, P14306
- Ligands
- ACE, NAG, SO4
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Carboxypeptidase Y (EC 3.4.16.5) | protein | 421 | 40% helix, 17% strand | P00729 |
| B | Carboxypeptidase Y inhibitor | protein | 204 | 17% helix, 33% strand | P14306 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.76 | 0.99 | 18 | SO4 |
| 2 | 216 | 0.51 | 0.76 | 33 | empty |
| 3 | 98 | 0.40 | 0.77 | 20 | empty |
| 4 | 106 | 0.39 | 0.75 | 19 | empty |
| 5 | 122 | 0.37 | 0.74 | 32 | empty |
Interfaces
1 interface between chains.
- A–B · 1657 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 1WPX · Crystal structure of carboxypeptidase Y inhibitor complexed with the cognate proteinase · the same entry in another collection · chain A against A, TM-score 1.00
- P00729 · AlphaFold monomer V2.0 prediction for carboxypeptidase Y (P00729) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P14306 · AlphaFold monomer V2.0 prediction for carboxypeptidase Y inhibitor (P14306) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P00729
- Every structure of UniProt P14306
- Elsewhere: RCSB PDB 1WPX · PDBe 1WPX · UniProt P00729 · UniProt P14306
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