Research workbench
Mechanism of sulfotyrosine-mediated glycoprotein ib interaction with two distinct alpha-thrombin sites
Analyse Mechanism of sulfotyrosine-mediated glycoprotein ib interaction with two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PMH
- Type
- protein
- Length
- 579 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin alpha-chain; Thrombin beta-chain; Platelet glycoprotein ib alpha chain
- EC
- 3.4.21.5
- UniProt
- P00734, P07359
- Ligands
- 0G7, NAG, MAN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin alpha-chain (EC 3.4.21.5) | protein | 36 | 31% helix, 0% strand | P00734 |
| B | Thrombin beta-chain (EC 3.4.21.5) | protein | 259 | 12% helix, 35% strand | P00734 |
| G | Platelet glycoprotein ib alpha chain | protein | 284 | 7% helix, 15% strand | P07359 |
Ligands and binding sites
- 0G7 · D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, G
- MAN · alpha-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1184 | 0.75 | 0.78 | 103 | 0G7 |
| 2 | 115 | 0.53 | 0.82 | 26 | empty |
| 3 | 153 | 0.52 | 0.80 | 23 | empty |
| 4 | 176 | 0.51 | 0.78 | 29 | empty |
| 5 | 81 | 0.39 | 0.77 | 20 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1390 Ų buried · 26 hydrogen bonds · protein-protein
- B–G · 1222 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 3 modified, 2 glycan (disulfide, sulfation, N-glycosylation).
Compared structures
- 3PMH · Mechanism of Sulfotyrosine-Mediated Glycoprotein Ib Interaction with Two Distinct… · 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 G against A, TM-score 0.94
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P00734
- Every structure of UniProt P07359
- Elsewhere: RCSB PDB 3PMH · PDBe 3PMH · UniProt P00734 · UniProt P07359
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