Research workbench
Crystal structure of the complex of platelet receptor gpib-alpha and alpha-thrombin at 2.6A
Analyse Crystal structure of the complex of platelet receptor gpib-alpha and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1P8V
- Type
- protein
- Length
- 558 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Platelet glycoprotein ib alpha chain; Prothrombin
- EC
- 3.4.21.5
- UniProt
- P07359, P00734
- Ligands
- DFP, NAG
- Pockets
- 4 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 14% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Platelet glycoprotein ib alpha chain | protein | 279 | 10% helix, 17% strand | P07359 |
| B | Prothrombin (EC 3.4.21.5) | protein | 29 | 38% helix, 0% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 35% strand | P00734 |
Ligands and binding sites
- DFP · Diisopropyl phosphonate · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.69 | 0.78 | 49 | MES |
| 2 | 248 | 0.54 | 0.77 | 38 | DFP |
| 3 | 109 | 0.38 | 0.75 | 22 | empty |
| 4 | 65 | 0.35 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1207 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1001 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 2 modified, 1 covalent, 1 glycan (disulfide, sulfation, covalent ligand, N-glycosylation).
Compared structures
- 1P8V · Crystal structure of the complex of platelet receptor gpib-alpha and alpha-thrombin at… · the same entry in another collection · chain A against A, TM-score 1.00
- P07359 · AlphaFold monomer V2.0 prediction for platelet glycoprotein ib alpha chain (P07359) · a predicted model of the same protein · chain A 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 P07359
- Every structure of UniProt P00734
- Elsewhere: RCSB PDB 1P8V · PDBe 1P8V · UniProt P07359 · UniProt P00734
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