Research workbench
Crystal structure of masp-1 CUB2 domain bound to CA2+
Analyse Crystal structure of masp-1 CUB2 domain bound to CA2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3POF
- Type
- protein
- Length
- 227 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan-binding lectin serine protease 1
- EC
- 3.4.21.-
- UniProt
- Q8CHN8
- Ligands
- CA, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mannan-binding lectin serine protease 1 (EC 3.4.21.-) | protein | 113 | 0% helix, 46% strand | Q8CHN8 |
| B | Mannan-binding lectin serine protease 1 (EC 3.4.21.-) | protein | 114 | 0% helix, 43% strand | Q8CHN8 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 258 | 0.62 | 0.81 | 40 | empty |
| 2 | 57 | 0.29 | 0.75 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 718 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 3POF · Crystal structure of MASP-1 CUB2 domain bound to Ca2+ · the same entry in another collection · chain A against A, TM-score 1.00
- Q8CHN8 · AlphaFold monomer V2.0 prediction for mannan-binding lectin serine protease 1 (Q8CHN8) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8CHN8
- Elsewhere: RCSB PDB 3POF · PDBe 3POF · UniProt Q8CHN8
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