Research workbench
Crystal structure of the CUB1-EGF-CUB2 region of MASP2
Analyse Crystal structure of the CUB1-EGF-CUB2 region of MASP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NT0
- Type
- protein
- Length
- 514 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding protein associated serine protease-2
- UniProt
- Q9JJS8
- Ligands
- NAG, CA
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, G | Mannose-binding protein associated serine protease-2 | protein | 257 | 1% helix, 48% strand | Q9JJS8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, G
- CA · Calcium ion · metal · 2 copies · chains A, G
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.39 | 0.75 | 15 | empty |
| 2 | 94 | 0.37 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–G · 952 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 1NT0 · Crystal structure of the CUB1-EGF-CUB2 region of MASP2 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JJS8 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 2 (Q9JJS8) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9JJS8
- Elsewhere: RCSB PDB 1NT0 · PDBe 1NT0 · UniProt Q9JJS8
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