MolNFT v2 · #111917 · protein
Crystal structure of full-length glypican-1 core protein after controlled crystal dehydration to 87% relative humidity
4YWT: “Crystal structure of full-length glypican-1 core protein after controlled crystal dehydration to 87% relative…”. X-ray diffraction at 2.38, 2 ligands (NAG, CA), 20 pockets (best druggability 0.69). MolNFT v2 #111917 on GenesisL1: 3D…
- PDB
- 4YWT
- Type
- protein
- Length
- 1,671 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.38
- Source
- Homo sapiens
- Molecule
- Glypican-1
- UniProt
- P35052
- Ligands
- NAG, CA
- Pockets
- 20 · best druggability 0.69
Structure
x-ray diffraction · resolution 2.38 · 4 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glypican-1 | protein | 411 | 65% helix, 3% strand | P35052 |
| B | Glypican-1 | protein | 431 | 66% helix, 3% strand | P35052 |
| C | Glypican-1 | protein | 400 | 67% helix, 3% strand | P35052 |
| D | Glypican-1 | protein | 429 | 66% helix, 3% 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 | 723 | 0.69 | 0.77 | 79 | CA |
| 2 | 640 | 0.68 | 0.77 | 71 | CA |
| 3 | 323 | 0.60 | 0.78 | 33 | empty |
| 4 | 55 | 0.60 | 0.91 | 15 | empty |
| 5 | 257 | 0.57 | 0.78 | 42 | empty |
Interfaces
2 interfaces between chains.
- C–D · 575 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 459 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4YWT · Crystal structure of full-length glypican-1 core protein after controlled crystal… · 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 4YWT · PDBe 4YWT · UniProt P35052
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