MolNFT v1 · #128884 · protein
Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to presegetalin A1
5O3W · Peptide cyclase 1: “Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to…”. X-ray diffraction, 2 ligands (MG, SO4), 20 pockets (best druggability 0.82). MolNFT v1 #128884 on…
- PDB
- 5O3W
- Type
- protein
- Length
- 2,871 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
- MG, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 7 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 709 | 23% helix, 32% strand | R4P353 |
| B | Peptide cyclase 1 | protein | 717 | 23% helix, 32% strand | R4P353 |
| C | Peptide cyclase 1 | protein | 716 | 22% helix, 32% strand | R4P353 |
| D | Peptide cyclase 1 | protein | 702 | 23% helix, 32% strand | R4P353 |
| W | Presegetalin A1 | protein | 7 | 0% helix, 0% strand | F6LNL5 |
| X, Y | Presegetalin A1 | protein | 6 | 0% helix, 0% strand | F6LNL5 |
| Z | Presegetalin A1 | protein | 8 | 0% helix, 0% strand | F6LNL5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 831 | 0.82 | 0.85 | 106 | empty |
| 2 | 931 | 0.77 | 0.80 | 94 | empty |
| 3 | 613 | 0.75 | 0.82 | 64 | empty |
| 4 | 585 | 0.71 | 0.79 | 50 | empty |
| 5 | 292 | 0.70 | 0.84 | 33 | empty |
Interfaces
8 interfaces between chains.
- A–B · 746 Ų buried · 2 hydrogen bonds · protein-protein
- D–Z · 617 Ų buried · 9 hydrogen bonds · protein-protein
- A–W · 548 Ų buried · 8 hydrogen bonds · protein-protein
- C–Y · 476 Ų buried · 12 hydrogen bonds · protein-protein
- B–X · 469 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5O3W · Structural characterization of the fast and promiscuous macrocyclase from plant… · 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 5O3W · PDBe 5O3W · UniProt R4P353 · UniProt F6LNL5
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