Research workbench
Crystal structure of ppep-1(W103F/E143A/Y178F) in complex with substrate peptide ac-evnppvp-CONH2
Analyse Crystal structure of ppep-1(W103F/E143A/Y178F) in complex with substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R5C
- Type
- protein
- Length
- 398 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-pro endopeptidase; ACE-glu-val-asn-pro-pro-val-lpd
- EC
- 3.4.24.89
- UniProt
- Q183R7
- Ligands
- ACE, ZN
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 193 | 54% helix, 8% strand | Q183R7 |
| B | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 191 | 53% helix, 8% strand | Q183R7 |
| C, D | ACE-glu-val-asn-pro-pro-val-lpd | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains A, C, B, D
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.50 | 0.74 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–C · 706 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 686 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 282 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 6R5C · Crystal structure of PPEP-1(W103F/E143A/Y178F) in complex with substrate peptide… · the same entry in another collection · chain A against A, TM-score 1.00
- Q183R7 · AlphaFold monomer V2.0 prediction for pro-pro endopeptidase (Q183R7) · a predicted model of the same protein · chain B 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 Q183R7
- Elsewhere: RCSB PDB 6R5C · PDBe 6R5C · UniProt Q183R7
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