Research workbench
Structure of the calcium-dependent lectin domain from a rat mannose-binding protein determined by mad phasing
Analyse Structure of the calcium-dependent lectin domain from a rat mannose-binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MSB
- Type
- protein
- Length
- 230 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mannose-binding protein-a
- UniProt
- P19999
- Ligands
- HO
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Mannose-binding protein-a | protein | 115 | 21% helix, 33% strand | P19999 |
Ligands and binding sites
- HO · Holmium atom · metal · 4 copies · chains A, B
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 | 70 | 0.33 | 0.76 | 19 | empty |
| 2 | 51 | 0.27 | 0.74 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 622 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1MSB · Structure of the calcium-dependent lectin domain from a rat mannose-binding protein… · the same entry in another collection · chain A against A, TM-score 1.00
- P19999 · AlphaFold monomer V2.0 prediction for mannose-binding protein a (P19999) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P19999
- Elsewhere: RCSB PDB 1MSB · PDBe 1MSB · UniProt P19999
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.