Research workbench
Glycoprotein gpib variant
Analyse Glycoprotein gpib variant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3REZ
- Type
- protein
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet glycoprotein ib beta chain, platelet glycoprotein IX
- UniProt
- P13224, P14770
- Ligands
- NAG, FUL, MAN
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet glycoprotein ib beta chain, platelet glycoprotein IX | protein | 113 | 25% helix, 17% strand | P13224, P14770 |
| B | Platelet glycoprotein ib beta chain, platelet glycoprotein IX | protein | 114 | 26% helix, 17% strand | P13224, P14770 |
| C | Platelet glycoprotein ib beta chain, platelet glycoprotein IX | protein | 116 | 25% helix, 16% strand | P13224, P14770 |
| D | Platelet glycoprotein ib beta chain, platelet glycoprotein IX | protein | 111 | 23% helix, 17% strand | P13224, P14770 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B, C, D
- FUL · beta-L-fucopyranose · sugar · chains B, C
- MAN · alpha-D-mannopyranose · sugar
- PEG · Di(hydroxyethyl)ether · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 625 | 0.74 | 0.81 | 79 | empty |
| 2 | 370 | 0.55 | 0.74 | 40 | empty |
| 3 | 90 | 0.35 | 0.75 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–C · 579 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 523 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 404 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 150 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3REZ · glycoprotein GPIb variant · the same entry in another collection · chain B against B, TM-score 1.00
- P14770 · AlphaFold monomer V2.0 prediction for platelet glycoprotein IX (P14770) · a predicted model of the same protein · chain D against A, TM-score 0.93
- P13224 · AlphaFold monomer V2.0 prediction for platelet glycoprotein ib beta chain (P13224) · a predicted model of the same protein · chain C against A, TM-score 0.89
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 P13224
- Every structure of UniProt P14770
- Elsewhere: RCSB PDB 3REZ · PDBe 3REZ · UniProt P13224 · UniProt P14770
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