MolNFT v1 · #136539 · protein
PCY1 Y481F variant in complex with follower peptide
5UW7 · Peptide cyclase 1: “PCY1 Y481F variant in complex with follower peptide”. X-ray diffraction, 1 ligand (MG), 13 pockets (best druggability 0.77). MolNFT v1 #136539 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UW7
- Type
- protein
- Length
- 1,334 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide cyclase 1; Presegetalin A1
- UniProt
- R4P353, F6LNL5
- Ligands
- MG
- Pockets
- 13 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 666 | 24% helix, 31% strand | R4P353 |
| C, D | Presegetalin A1 | protein | 6 | 0% helix, 0% strand | F6LNL5 |
| B | Peptide cyclase 1 | protein | 656 | 23% helix, 32% strand | R4P353 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 762 | 0.77 | 0.81 | 99 | empty |
| 2 | 570 | 0.75 | 0.82 | 60 | empty |
| 3 | 762 | 0.74 | 0.79 | 61 | empty |
| 4 | 436 | 0.66 | 0.79 | 64 | empty |
| 5 | 180 | 0.55 | 0.79 | 30 | empty |
Interfaces
3 interfaces between chains.
- A–B · 608 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 458 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 455 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5UW7 · PCY1 Y481F Variant in Complex with Follower Peptide · 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 5UW7 · PDBe 5UW7 · UniProt R4P353 · UniProt F6LNL5
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