Research workbench
Crystal structure of ergic-53/MCFD2, trigonal calcium-bound form 2
Analyse Crystal structure of ergic-53/MCFD2, trigonal calcium-bound form 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YGE
- Type
- protein
- Length
- 872 residues
- Chains
- 6
- 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
- 9 · best druggability 0.66
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein ergic-53 | protein | 227 | 3% helix, 46% strand | P49257 |
| B, D | Multiple coagulation factor deficiency protein 2 | protein | 66 | 59% helix, 9% strand | Q8NI22 |
| C | Protein ergic-53 | protein | 223 | 5% helix, 47% strand | P49257 |
| E | Protein ergic-53 | protein | 223 | 1% helix, 48% strand | P49257 |
| F | Multiple coagulation factor deficiency protein 2 | protein | 67 | 58% helix, 9% strand | Q8NI22 |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D, F
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.66 | 0.76 | 47 | empty |
| 2 | 304 | 0.65 | 0.81 | 43 | empty |
| 3 | 264 | 0.60 | 0.79 | 45 | CL |
| 4 | 73 | 0.55 | 0.87 | 19 | CL |
| 5 | 62 | 0.53 | 0.87 | 19 | CL |
Interfaces
6 interfaces between chains.
- E–F · 862 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 797 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 791 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 582 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 204 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4YGE · Crystal structure of ERGIC-53/MCFD2, trigonal calcium-bound form 2 · the same entry in another collection · chain F against F, 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 F against A, TM-score 0.98
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 4YGE · PDBe 4YGE · UniProt P49257 · UniProt Q8NI22
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