MolNFT v1 · #20023 · protein
The crystal structure of the carbohydrate recognition domain of the glycoprotein sorting receptor P58/ERGIC-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding
1R1Z · Ergic-53 protein: “The crystal structure of the carbohydrate recognition domain of the glycoprotein sorting receptor…”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.69). MolNFT v1 #20023 on GenesisL1: 3D…
- PDB
- 1R1Z
- Type
- protein
- Length
- 988 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ergic-53 protein
- UniProt
- Q62902
- Ligands
- CA
- Pockets
- 9 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 6% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Ergic-53 protein | protein | 247 | 6% helix, 42% strand | Q62902 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 388 | 0.69 | 0.81 | 52 | empty |
| 2 | 437 | 0.65 | 0.78 | 39 | empty |
| 3 | 238 | 0.56 | 0.78 | 33 | empty |
| 4 | 120 | 0.43 | 0.77 | 28 | empty |
| 5 | 143 | 0.40 | 0.74 | 25 | empty |
Interfaces
3 interfaces between chains.
- B–C · 499 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 358 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 233 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1R1Z · The Crystal structure of the Carbohydrate recognition domain of the glycoprotein sorting… · the same entry in another collection · chain A against A, TM-score 1.00
- Q62902 · AlphaFold monomer V2.0 prediction for protein ergic-53 (Q62902) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q62902
- Elsewhere: RCSB PDB 1R1Z · PDBe 1R1Z · UniProt Q62902
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