MolNFT v1 · #128885 · protein
Structural characterization of the fast and promiscuous macrocyclase from plant - apo PCY1
5O3X · Peptide cyclase 1: “Structural characterization of the fast and promiscuous macrocyclase from plant - apo PCY1”. X-ray diffraction, 18 pockets (best druggability 0.81). MolNFT v1 #128885 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5O3X
- Type
- protein
- Length
- 1,420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide cyclase 1
- UniProt
- R4P353
- Pockets
- 18 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 714 | 23% helix, 32% strand | R4P353 |
| B | Peptide cyclase 1 | protein | 706 | 23% helix, 32% strand | R4P353 |
Ligands and binding sites
- CAC · Cacodylate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1169 | 0.81 | 0.82 | 136 | empty |
| 2 | 1095 | 0.78 | 0.80 | 114 | CAC |
| 3 | 776 | 0.77 | 0.81 | 85 | CAC |
| 4 | 512 | 0.70 | 0.80 | 51 | empty |
| 5 | 311 | 0.63 | 0.80 | 44 | empty |
Interfaces
1 interface between chains.
- A–B · 711 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O3X · Structural characterization of the fast and promiscuous macrocyclase from plant - apo PCY1 · 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
- Elsewhere: RCSB PDB 5O3X · PDBe 5O3X · UniProt R4P353
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