MolNFT v1 · #162309 · protein
Crystal structure of apo ppep-1(E143A/Y178F) in complex with fibrinogen-derived substrate peptide ac-slrpapp-CONH2
6R51 · Pro-pro endopeptidase: “Crystal structure of apo ppep-1(E143A/Y178F) in complex with fibrinogen-derived substrate peptide…”. X-ray diffraction, 2 ligands (ACE, PO4), 3 pockets (best druggability 0.70). MolNFT v1 #162309 on…
- PDB
- 6R51
- Type
- protein
- Length
- 609 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pro-pro endopeptidase; ACE-ser-leu-arg-pro-ala-pro-lpd
- EC
- 3.4.24.89
- UniProt
- Q183R7
- Ligands
- ACE, PO4
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 196 | 57% helix, 8% strand | Q183R7 |
| E, D, F | ACE-ser-leu-arg-pro-ala-pro-lpd | protein | 7 | 0% helix, 43% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains B, E, A, D, C, F
- PO4 · Phosphate ion · ion · chains A
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 | 258 | 0.70 | 0.85 | 35 | empty |
| 2 | 189 | 0.47 | 0.75 | 37 | empty |
| 3 | 76 | 0.27 | 0.71 | 14 | PO4 |
Interfaces
6 interfaces between chains.
- B–E · 739 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 698 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 697 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 582 Ų buried · 9 hydrogen bonds · protein-protein
- B–A · 568 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent, 3 modified (covalent ligand, nonstandard).
Compared structures
- 6R51 · Crystal structure of apo PPEP-1(E143A/Y178F) in complex with fibrinogen-derived substrate… · 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 0.98
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 6R51 · PDBe 6R51 · UniProt Q183R7
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