MolNFT v1 · #162307 · protein
Crystal structure of holo ppep-1(E143A/Y178F) in complex with product peptide ac-evnp-CO2 (substrate peptide: ac-evnppvp-CONH2)
6R4Z · Pro-pro endopeptidase: “Crystal structure of holo ppep-1(E143A/Y178F) in complex with product peptide ac-evnp-CO2 (substrate peptide…”. X-ray diffraction, 3 ligands (ACE, ZN, NI), 2 pockets (best druggability 0.75). MolNFT v1…
- PDB
- 6R4Z
- 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
- EC
- 3.4.24.89
- UniProt
- Q183R7
- Ligands
- ACE, ZN, NI
- Pockets
- 2 · best druggability 0.75
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 | 198 | 53% helix, 8% strand | Q183R7 |
| B | Pro-pro endopeptidase (EC 3.4.24.89) | protein | 192 | 55% helix, 8% strand | Q183R7 |
| D, E | ACE-glu-val-asn-pro | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, D, A, E
- ZN · Zinc ion · metal · 2 copies · chains A, E, B, D
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.75 | 0.85 | 76 | empty |
| 2 | 71 | 0.30 | 0.74 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 667 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 435 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 424 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6R4Z · Crystal structure of holo PPEP-1(E143A/Y178F) in complex with product peptide Ac-EVNP-CO2… · 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 0.99
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 6R4Z · PDBe 6R4Z · UniProt Q183R7
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