Research workbench
Crystal structure of DPR1 IG1 bound to dip-eta IG1
Analyse Crystal structure of DPR1 IG1 bound to dip-eta IG1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NRW
- Type
- protein
- Length
- 424 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DPR1; Dpr-interacting protein eta, isoform B
- UniProt
- Q8T603, Q9VMN9
- Ligands
- NAG, FUC, BMA, SO4
- Pockets
- 1 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DPR1 | protein | 108 | 3% helix, 47% strand | Q8T603 |
| B, D | Dpr-interacting protein eta, isoform B | protein | 105 | 3% helix, 50% strand | Q9VMN9 |
| C | DPR1 | protein | 106 | 3% helix, 48% strand | Q8T603 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, D
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 3 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.81 | 0.82 | 74 | empty |
Interfaces
5 interfaces between chains.
- A–B · 918 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 917 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 333 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 265 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6NRW · Crystal structure of Dpr1 IG1 bound to DIP-eta IG1 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8T603
- Every structure of UniProt Q9VMN9
- Elsewhere: RCSB PDB 6NRW · PDBe 6NRW · UniProt Q8T603 · UniProt Q9VMN9
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