MolNFT v1 · #128882 · protein
Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to presegetalin F1
5O3U · Peptide cyclase 1: “Structural characterization of the fast and promiscuous macrocyclase from plant - PCY1-S562A bound to…”. X-ray diffraction, 20 pockets (best druggability 0.85). MolNFT v1 #128882 on GenesisL1: 3D structure…
- PDB
- 5O3U
- Type
- protein
- Length
- 2,901 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peptide cyclase 1; Putative presegetalin F1
- UniProt
- R4P353, F6LNM3
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 711 | 23% helix, 31% strand | R4P353 |
| B | Peptide cyclase 1 | protein | 703 | 23% helix, 33% strand | R4P353 |
| C | Peptide cyclase 1 | protein | 706 | 23% helix, 33% strand | R4P353 |
| D | Peptide cyclase 1 | protein | 710 | 23% helix, 31% strand | R4P353 |
| L | Putative presegetalin F1 | protein | 18 | 0% helix, 0% strand | F6LNM3 |
| M, O | Putative presegetalin F1 | protein | 18 | 0% helix, 0% strand | F6LNM3 |
| N | Putative presegetalin F1 | protein | 17 | 0% helix, 0% strand | F6LNM3 |
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1064 | 0.85 | 0.86 | 88 | empty |
| 2 | 825 | 0.85 | 0.88 | 89 | empty |
| 3 | 867 | 0.85 | 0.87 | 120 | empty |
| 4 | 796 | 0.84 | 0.87 | 93 | empty |
| 5 | 757 | 0.84 | 0.87 | 83 | empty |
Interfaces
9 interfaces between chains.
- B–M · 1384 Ų buried · 30 hydrogen bonds · protein-protein
- D–O · 1361 Ų buried · 27 hydrogen bonds · protein-protein
- A–L · 1346 Ų buried · 31 hydrogen bonds · protein-protein
- C–N · 1319 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5O3U · 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 F6LNM3
- Elsewhere: RCSB PDB 5O3U · PDBe 5O3U · UniProt R4P353 · UniProt F6LNM3
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