Research workbench
PCY1 G696INSERTION variant in complex with follower peptide and the covalent inhibitor zpp
Analyse PCY1 G696INSERTION variant in complex with follower peptide and the covalent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UZW
- Type
- protein
- Length
- 2,793 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 0.78
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 686 | 24% helix, 31% strand | R4P353 |
| E, F, G, H | Presegetalin A1 | protein | 6 | 0% helix, 0% strand | F6LNL5 |
| B | Peptide cyclase 1 | protein | 701 | 24% helix, 30% strand | R4P353 |
| C | Peptide cyclase 1 | protein | 697 | 23% helix, 31% strand | R4P353 |
| D | Peptide cyclase 1 | protein | 685 | 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 · 3 copies · chains A, B
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 | 838 | 0.78 | 0.81 | 76 | empty |
| 2 | 1120 | 0.78 | 0.80 | 111 | empty |
| 3 | 873 | 0.76 | 0.79 | 86 | ZPR |
| 4 | 764 | 0.73 | 0.79 | 58 | empty |
| 5 | 581 | 0.72 | 0.80 | 81 | empty |
Interfaces
9 interfaces between chains.
- A–C · 803 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 725 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 647 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 478 Ų buried · 12 hydrogen bonds · protein-protein
- D–H · 473 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5UZW · PCY1 G696Insertion Variant in Complex with Follower Peptide and the 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 5UZW · PDBe 5UZW · UniProt R4P353 · UniProt F6LNL5
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