MolNFT v1 · #162316 · protein
Crystal structure of ppep-1(E143A/Y178F/E184A) in complex with substrate peptide ac-evnapvp-CONH2
6R58 · Pro-pro endopeptidase: “Crystal structure of ppep-1(E143A/Y178F/E184A) in complex with substrate peptide ac-evnapvp-CONH2”. X-ray diffraction, 4 ligands (ACE, ZN, NI), 3 pockets (best druggability 0.77). MolNFT v1 #162316 on…
- PDB
- 6R58
- Type
- protein
- Length
- 802 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-pro endopeptidase; ACE-glu-val-asn-ala-pro-val-lpd
- EC
- 3.4.24.89
- UniProt
- Q183R7
- Ligands
- ACE, ZN, NI, PO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 192 | 56% helix, 8% strand | Q183R7 |
| D | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 198 | 52% helix, 8% strand | Q183R7 |
| E, F, I, G | ACE-glu-val-asn-ala-pro-val-lpd | protein | 7 | 0% helix, 29% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, C, E, B, F, I, D, G
- ZN · Zinc ion · metal · 3 copies · chains A, E, C, I, D, G
- NI · Nickel (II) ion · metal · chains D
- PO4 · Phosphate ion · ion · chains B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.77 | 0.79 | 148 | ACE |
| 2 | 55 | 0.36 | 0.79 | 14 | empty |
| 3 | 62 | 0.34 | 0.77 | 17 | empty |
Interfaces
13 interfaces between chains.
- B–F · 671 Ų buried · 10 hydrogen bonds · protein-protein
- D–G · 670 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 666 Ų buried · 9 hydrogen bonds · protein-protein
- C–I · 654 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 311 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 4 modified (covalent ligand, nonstandard).
Compared structures
- 6R58 · Crystal structure of PPEP-1(E143A/Y178F/E184A) in complex with substrate peptide… · the same entry in another collection · chain G against G, TM-score 1.00
- Q183R7 · AlphaFold monomer V2.0 prediction for pro-pro endopeptidase (Q183R7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 6R58 · PDBe 6R58 · UniProt Q183R7
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