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Crystal structure of C-terminally truncated glypican-1 after controlled dehydration to 86 percent relative humidity
Analyse Crystal structure of C-terminally truncated glypican-1 after controlled… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BWE
- Type
- protein
- Length
- 1,644 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glypican-1
- UniProt
- P35052
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glypican-1 | protein | 402 | 67% helix, 2% strand | P35052 |
| B | Glypican-1 | protein | 422 | 67% helix, 3% strand | P35052 |
| C | Glypican-1 | protein | 399 | 66% helix, 3% strand | P35052 |
| D | Glypican-1 | protein | 421 | 65% helix, 2% strand | P35052 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.73 | 0.77 | 106 | CA |
| 2 | 718 | 0.69 | 0.77 | 78 | CA |
| 3 | 77 | 0.66 | 0.92 | 17 | empty |
| 4 | 71 | 0.58 | 0.89 | 17 | empty |
| 5 | 72 | 0.57 | 0.88 | 17 | empty |
Interfaces
2 interfaces between chains.
- C–D · 532 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 497 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4BWE · Crystal structure of C-terminally truncated glypican-1 after controlled dehydration to 86… · the same entry in another collection · chain D against D, TM-score 1.00
- P35052 · AlphaFold monomer V2.0 prediction for glypican-1 (P35052) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P35052
- Elsewhere: RCSB PDB 4BWE · PDBe 4BWE · UniProt P35052
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