Research workbench
PCY1 in complex with follower peptide and covalent inhibitor zpp
Analyse PCY1 in complex with follower peptide and covalent inhibitor zpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UW6
- Type
- protein
- Length
- 2,821 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide cyclase 1; Presegetalin A1
- UniProt
- R4P353, F6LNL5
- Ligands
- ZPR, CA
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 693 | 24% helix, 31% strand | R4P353 |
| E, F, G, H | Presegetalin A1 | protein | 6 | 0% helix, 0% strand | F6LNL5 |
| B | Peptide cyclase 1 | protein | 706 | 24% helix, 30% strand | R4P353 |
| C | Peptide cyclase 1 | protein | 701 | 23% helix, 31% strand | R4P353 |
| D | Peptide cyclase 1 | protein | 697 | 23% helix, 31% strand | R4P353 |
Ligands and binding sites
- ZPR · N-benzyloxycarbonyl-L-prolyl-L-prolinal · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 978 | 0.80 | 0.82 | 113 | ZPR |
| 2 | 1035 | 0.80 | 0.82 | 96 | empty |
| 3 | 993 | 0.76 | 0.79 | 74 | empty |
| 4 | 830 | 0.76 | 0.80 | 87 | empty |
| 5 | 755 | 0.75 | 0.80 | 62 | empty |
Interfaces
9 interfaces between chains.
- A–C · 760 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 709 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 632 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 471 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 468 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5UW6 · PCY1 in Complex with Follower Peptide and Covalent Inhibitor ZPP · 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 R4P353
- Every structure of UniProt F6LNL5
- Elsewhere: RCSB PDB 5UW6 · PDBe 5UW6 · UniProt R4P353 · UniProt F6LNL5
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