MolNFT v1 · #136537 · protein
PCY1 H695A variant in complex with follower peptide
5UW5 · Peptide cyclase 1: “PCY1 H695A variant in complex with follower peptide”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.81). MolNFT v1 #136537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5UW5
- Type
- protein
- Length
- 2,824 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
- CA
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 23% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peptide cyclase 1 | protein | 696 | 23% helix, 31% strand | R4P353 |
| E, F, G, H | Presegetalin A1 | protein | 6 | 0% helix, 0% strand | F6LNL5 |
| B | Peptide cyclase 1 | protein | 705 | 24% helix, 31% strand | R4P353 |
| C | Peptide cyclase 1 | protein | 702 | 23% helix, 30% strand | R4P353 |
| D | Peptide cyclase 1 | protein | 697 | 23% helix, 31% strand | R4P353 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B, C
- CAC · Cacodylate ion · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1029 | 0.81 | 0.82 | 95 | empty |
| 2 | 1129 | 0.79 | 0.81 | 91 | empty |
| 3 | 802 | 0.78 | 0.81 | 94 | empty |
| 4 | 681 | 0.77 | 0.82 | 98 | CAC |
| 5 | 852 | 0.75 | 0.79 | 84 | empty |
Interfaces
9 interfaces between chains.
- A–C · 768 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 690 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 642 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 479 Ų buried · 5 hydrogen bonds · protein-protein
- B–F · 465 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5UW5 · PCY1 H695A 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 5UW5 · PDBe 5UW5 · UniProt R4P353 · UniProt F6LNL5
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