MolNFT v1 · #190965 · protein
S580A with 18MER
7ZB1 · Prolyl endopeptidase: “S580A with 18MER”. X-ray diffraction, 2 ligands (BCT, NA), 20 pockets (best druggability 0.85). MolNFT v1 #190965 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ZB1
- Type
- protein
- Length
- 2,916 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase; 18MER
- Ligands
- BCT, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase | protein | 719 | 22% helix, 32% strand | — |
| B | Prolyl endopeptidase | protein | 725 | 22% helix, 33% strand | — |
| C | Prolyl endopeptidase | protein | 721 | 22% helix, 33% strand | — |
| D | Prolyl endopeptidase | protein | 724 | 22% helix, 32% strand | — |
| E, F, G | 18MER | protein | 7 | 0% helix, 0% strand | — |
| H | 18MER | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- BCT · Bicarbonate ion · ligand · 4 copies · chains C, D
- NA · Sodium ion · metal · 16 copies · chains A, B, C, D, H
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, D, C
- GOL · Glycerol · additive · chains C
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 | 983 | 0.85 | 0.86 | 111 | empty |
| 2 | 870 | 0.83 | 0.86 | 89 | empty |
| 3 | 558 | 0.77 | 0.84 | 60 | empty |
| 4 | 692 | 0.75 | 0.80 | 67 | empty |
| 5 | 760 | 0.74 | 0.79 | 69 | EDO |
Interfaces
9 interfaces between chains.
- A–D · 933 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 821 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 762 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 750 Ų buried · 9 hydrogen bonds · protein-protein
- C–G · 602 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (methylation, nonstandard).
Compared structures
- 7ZB1 · S580A with 18mer · 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 7ZB1 · PDBe 7ZB1
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