Research workbench
Crystal structure of the autoprocessed complex of vibriolysin mcp-02 with a single point mutation E346A
Analyse Crystal structure of the autoprocessed complex of vibriolysin mcp-02 with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NQY
- Type
- protein
- Length
- 481 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Secreted metalloprotease MCP02
- EC
- 3.4.24.25
- UniProt
- A1DRD5
- Ligands
- CA, ZN
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Secreted metalloprotease MCP02 (EC 3.4.24.25) | protein | 307 | 39% helix, 16% strand | A1DRD5 |
| A | Secreted metalloprotease MCP02 (EC 3.4.24.25) | protein | 174 | 18% helix, 46% strand | A1DRD5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.69 | 0.78 | 52 | empty |
| 2 | 107 | 0.54 | 0.83 | 25 | empty |
| 3 | 108 | 0.48 | 0.80 | 23 | empty |
| 4 | 53 | 0.36 | 0.79 | 16 | empty |
| 5 | 51 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- B–A · 1579 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3NQY · Crystal structure of the autoprocessed complex of Vibriolysin MCP-02 with a single point… · the same entry in another collection · chain B against B, 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
- Every structure of UniProt A1DRD5
- Elsewhere: RCSB PDB 3NQY · PDBe 3NQY · UniProt A1DRD5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.