MolNFT v1 · #190964 · protein
Macrocyclase ophp with 15MER
7ZB0 · Prolyl endopeptidase: “Macrocyclase ophp with 15MER”. X-ray diffraction, 2 ligands (BCT, NA), 20 pockets (best druggability 0.79). MolNFT v1 #190964 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ZB0
- Type
- protein
- Length
- 2,891 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase; 15MER
- Ligands
- BCT, NA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase | protein | 720 | 23% helix, 32% strand | — |
| B | Prolyl endopeptidase | protein | 718 | 22% helix, 33% strand | — |
| C | Prolyl endopeptidase | protein | 706 | 23% helix, 33% strand | — |
| D | Prolyl endopeptidase | protein | 719 | 23% helix, 32% strand | — |
| E, G | 15MER | protein | 5 | 0% helix, 0% strand | — |
| F | 15MER | protein | 7 | 0% helix, 0% strand | — |
| H | 15MER | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · chains B
- NA · Sodium ion · metal · 6 copies · chains C, D
- EDO · 1,2-ethanediol · additive · 6 copies · chains B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.79 | 0.82 | 80 | empty |
| 2 | 737 | 0.79 | 0.83 | 73 | NA |
| 3 | 894 | 0.75 | 0.79 | 74 | empty |
| 4 | 613 | 0.75 | 0.81 | 63 | empty |
| 5 | 907 | 0.75 | 0.78 | 72 | empty |
Interfaces
8 interfaces between chains.
- A–D · 836 Ų buried · 7 hydrogen bonds · protein-protein
- D–H · 747 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 732 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 570 Ų buried · 1 hydrogen bond · protein-protein
- C–G · 467 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (methylation, nonstandard).
Compared structures
- 7ZB0 · macrocyclase OphP with 15mer · 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
- Elsewhere: RCSB PDB 7ZB0 · PDBe 7ZB0
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