MolNFT v1 · #191111 · protein
Second crystal form of the mature glutamic-class prolyl-endopeptidase neprosin at 1.85 a resolution.
7ZVC · C-terminal peptidase: “Second crystal form of the mature glutamic-class prolyl-endopeptidase neprosin at 1.85 a resolution.”. X-ray diffraction, 5 ligands (GLY, NAG, BMA), 1 pocket (best druggability 0.37). MolNFT v1 #191111 on…
- PDB
- 7ZVC
- Type
- protein
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- C-terminal peptidase; Gly-gly-gly-gly
- Ligands
- GLY, NAG, BMA, NI, SO4
- Pockets
- 1 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | C-terminal peptidase | protein | 257 | 6% helix, 40% strand | — |
| C | Gly-gly-gly-gly | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- GLY · Glycine · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- NI · Nickel (II) ion · metal · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.37 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–C · 255 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 7ZVC · Second crystal form of the mature glutamic-class prolyl-endopeptidase neprosin at 1.85 A… · 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 7ZVC · PDBe 7ZVC
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