Research workbench
Crystal structure of ergic-53/MCFD2, CALCIUM/MAN2-bound form
Analyse Crystal structure of ergic-53/MCFD2, CALCIUM/MAN2-bound form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WHU
- Type
- protein
- Length
- 284 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein ergic-53; Multiple coagulation factor deficiency protein 2
- UniProt
- P49257, Q8NI22
- Ligands
- MAN, CA
- Pockets
- 2 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 15% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ergic-53 | protein | 226 | 4% helix, 46% strand | P49257 |
| B | Multiple coagulation factor deficiency protein 2 | protein | 58 | 57% helix, 3% strand | Q8NI22 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 57 | 0.58 | 0.90 | 20 | GOL |
| 2 | 179 | 0.42 | 0.73 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 783 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3WHU · Crystal structure of ERGIC-53/MCFD2, Calcium/Man2-bound form · the same entry in another collection · chain A against A, TM-score 1.00
- P49257 · AlphaFold monomer V2.0 prediction for protein ergic-53 (P49257) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q8NI22 · AlphaFold monomer V2.0 prediction for multiple coagulation factor deficiency protein 2… · a predicted model of the same protein · chain B 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 P49257
- Every structure of UniProt Q8NI22
- Elsewhere: RCSB PDB 3WHU · PDBe 3WHU · UniProt P49257 · UniProt Q8NI22
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