Research workbench
Site-2 protease from methanocaldococcus jannaschii
Analyse Site-2 protease from methanocaldococcus jannaschii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3B4R
- Type
- protein
- Length
- 434 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative zinc metalloprotease MJ0392
- EC
- 3.4.24.-
- UniProt
- Q57837
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative zinc metalloprotease MJ0392 (EC 3.4.24.-) | protein | 218 | 67% helix, 10% strand | Q57837 |
| B | Putative zinc metalloprotease MJ0392 (EC 3.4.24.-) | protein | 216 | 62% helix, 10% strand | Q57837 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 669 | 0.82 | 0.86 | 46 | empty |
| 2 | 1089 | 0.77 | 0.78 | 100 | ZN |
| 3 | 158 | 0.49 | 0.78 | 22 | empty |
| 4 | 98 | 0.43 | 0.78 | 20 | empty |
| 5 | 62 | 0.35 | 0.76 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1318 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 Q57837
- Elsewhere: RCSB PDB 3B4R · PDBe 3B4R · UniProt Q57837
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