Research workbench
Crystal structure of ERP29 D-domain in complex with the P-domain of calreticulin
Analyse Crystal structure of ERP29 D-domain in complex with the P-domain of calreticulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V90
- Type
- protein
- Length
- 244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoplasmic reticulum resident protein 29; Calreticulin
- UniProt
- P30040, P27797
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Endoplasmic reticulum resident protein 29 | protein | 97 | 81% helix, 0% strand | P30040 |
| B | Calreticulin | protein | 27 | 0% helix, 7% strand | P27797 |
| D | Calreticulin | protein | 23 | 0% helix, 0% strand | P27797 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 141 | 0.47 | 0.77 | 21 | empty |
| 2 | 117 | 0.42 | 0.76 | 22 | empty |
| 3 | 117 | 0.40 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 695 Ų buried · 10 hydrogen bonds · protein-protein
- C–A · 608 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 552 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5V90 · Crystal structure of ERp29 D-domain in complex with the P-domain of calreticulin · the same entry in another collection · chain D against D, TM-score 1.00
- P30040 · AlphaFold monomer V2.0 prediction for endoplasmic reticulum resident protein 29 (P30040) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P27797 · AlphaFold monomer V2.0 prediction for calreticulin (P27797) · a predicted model of the same protein · chain B against A, TM-score 0.69
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 P30040
- Every structure of UniProt P27797
- Elsewhere: RCSB PDB 5V90 · PDBe 5V90 · UniProt P30040 · UniProt P27797
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