MolNFT v1 · #115464 · protein
The CUB1-EGF-CUB2 domains of rat mbl-associated serine protease-2 (masp-2) bound to CA2+
5CKN · Mannan-binding lectin serine peptidase 2: “The CUB1-EGF-CUB2 domains of rat mbl-associated serine protease-2 (masp-2) bound to CA2+”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.54). MolNFT v1 #115464 on…
- PDB
- 5CKN
- Type
- protein
- Length
- 556 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannan-binding lectin serine peptidase 2
- UniProt
- A2VCV7
- Ligands
- CA
- Pockets
- 3 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Mannan-binding lectin serine peptidase 2 | protein | 278 | 1% helix, 45% strand | A2VCV7 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.54 | 0.75 | 32 | empty |
| 2 | 170 | 0.39 | 0.72 | 30 | empty |
| 3 | 103 | 0.33 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–D · 1201 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5CKN · The CUB1-EGF-CUB2 domains of rat MBL-associated serine protease-2 (MASP-2) bound to Ca2+ · 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 A2VCV7
- Elsewhere: RCSB PDB 5CKN · PDBe 5CKN · UniProt A2VCV7
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