MolNFT v1 · #111089 · protein
Crystal structure of ergic-53/MCFD2, monoclinic calcium-free form
4YGB · Protein ergic-53: “Crystal structure of ergic-53/MCFD2, monoclinic calcium-free form”. X-ray diffraction, 1 ligand (CA), 6 pockets (best druggability 0.57). MolNFT v1 #111089 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 4YGB
- Type
- protein
- Length
- 510 residues
- Chains
- 4
- 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
- Pockets
- 6 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Protein ergic-53 | protein | 192 | 2% helix, 53% strand | P49257 |
| B, D | Multiple coagulation factor deficiency protein 2 | protein | 63 | 59% helix, 10% strand | Q8NI22 |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains B, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.57 | 0.78 | 43 | GOL |
| 2 | 210 | 0.53 | 0.78 | 38 | GOL |
| 3 | 86 | 0.32 | 0.73 | 20 | empty |
| 4 | 81 | 0.32 | 0.74 | 20 | empty |
| 5 | 70 | 0.30 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 865 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 862 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 622 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4YGB · Crystal structure of ERGIC-53/MCFD2, monoclinic 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 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 0.95
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 4YGB · PDBe 4YGB · UniProt P49257 · UniProt Q8NI22
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