Research workbench
Crystal structure of ergic-53/MCFD2, calcium-free form
Analyse Crystal structure of ergic-53/MCFD2, calcium-free form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WHT
- Type
- protein
- Length
- 269 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
- CA, CL
- Pockets
- 2 · best druggability 0.50
Structure
x-ray diffraction · 2 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ergic-53 | protein | 208 | 1% helix, 50% strand | P49257 |
| B | Multiple coagulation factor deficiency protein 2 | protein | 61 | 57% helix, 3% strand | Q8NI22 |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains B
- CL · Chloride ion · ion · chains A, B
- GOL · Glycerol · additive · 2 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 | 121 | 0.50 | 0.80 | 25 | GOL |
| 2 | 158 | 0.41 | 0.73 | 25 | CL |
Interfaces
1 interface between chains.
- A–B · 797 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3WHT · Crystal structure of ERGIC-53/MCFD2, Calcium-free 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 0.99
- 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 0.93
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 3WHT · PDBe 3WHT · UniProt P49257 · UniProt Q8NI22
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