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Crystal structure of the metallopeptidase zymogen of methanocaldococcus jannaschii jannalysin
Analyse Crystal structure of the metallopeptidase zymogen of methanocaldococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JIX
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Projannalysin
- UniProt
- Q57587
- Ligands
- ZN, SO4, CL
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Projannalysin | protein | 112 | 50% helix, 13% strand | Q57587 |
| B | Projannalysin | protein | 104 | 54% helix, 13% strand | Q57587 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
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 | 67 | 0.65 | 0.93 | 20 | GOL |
| 2 | 65 | 0.44 | 0.82 | 15 | GOL |
| 3 | 70 | 0.42 | 0.80 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1031 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4JIX · Crystal structure of the metallopeptidase zymogen of Methanocaldococcus jannaschii… · the same entry in another collection · chain A against A, TM-score 1.00
- Q57587 · AlphaFold monomer V2.0 prediction for uncharacterized protein MJ0123 (Q57587) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q57587
- Elsewhere: RCSB PDB 4JIX · PDBe 4JIX · UniProt Q57587
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