Research workbench
CUB1-EGF-CUB2 domain of human masp-1/3
Analyse CUB1-EGF-CUB2 domain of human masp-1/3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DEM
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Complement factor masp-3
- EC
- 3.4.21.-
- UniProt
- Q96RS4
- Ligands
- NAG, CA
- Pockets
- 3 · best druggability 0.37
Structure
x-ray diffraction · 2 distinct chains · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Complement factor masp-3 (EC 3.4.21.-) | protein | 267 | 1% helix, 44% strand | Q96RS4 |
| B | Complement factor masp-3 (EC 3.4.21.-) | protein | 265 | 1% helix, 46% strand | Q96RS4 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CA · Calcium ion · metal · 6 copies · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.37 | 0.74 | 17 | empty |
| 2 | 59 | 0.30 | 0.75 | 15 | empty |
| 3 | 57 | 0.29 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1073 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3DEM · CUB1-EGF-CUB2 domain of HUMAN MASP-1/3 · 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
- Every structure of UniProt Q96RS4
- Elsewhere: RCSB PDB 3DEM · PDBe 3DEM · UniProt Q96RS4
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