Research workbench
Low-salt crystal structure of a thrombin-gpibalpha peptide complex
Analyse Low-salt crystal structure of a thrombin-gpibalpha peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CH2
- Type
- protein
- Length
- 585 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin, light chain; Thrombin, heavy chain; Platelet glycoprotein ib alpha chain…
- EC
- 3.4.21.5
- UniProt
- P00734, P07359
- Ligands
- 0G6, NA
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin, light chain (EC 3.4.21.5) | protein | 32 | 31% helix, 0% strand | P00734 |
| B | Thrombin, heavy chain (EC 3.4.21.5) | protein | 258 | 14% helix, 35% strand | P00734 |
| C | Thrombin, light chain (EC 3.4.21.5) | protein | 29 | 41% helix, 0% strand | P00734 |
| D | Thrombin, heavy chain (EC 3.4.21.5) | protein | 251 | 14% helix, 35% strand | P00734 |
| P | Platelet glycoprotein ib alpha chain, residues 287-300 | protein | 7 | 0% helix, 0% strand | P07359 |
| Q | Platelet glycoprotein ib alpha chain, residues 287-300 | protein | 8 | 0% helix, 0% strand | P07359 |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · 2 copies · chains B, D
- NA · Sodium ion · metal · 2 copies · chains B, D
- GOL · Glycerol · additive · 4 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 325 | 0.60 | 0.78 | 44 | 0G6 |
| 2 | 293 | 0.58 | 0.78 | 43 | 0G6 |
| 3 | 73 | 0.55 | 0.87 | 23 | empty |
| 4 | 134 | 0.49 | 0.79 | 21 | GOL |
| 5 | 60 | 0.31 | 0.75 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1385 Ų buried · 33 hydrogen bonds · protein-protein
- C–D · 1150 Ų buried · 26 hydrogen bonds · protein-protein
- D–Q · 660 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 538 Ų buried · 4 hydrogen bonds · protein-protein
- B–P · 502 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 6 modified, 4 covalent (disulfide, phosphorylation, covalent ligand).
Compared structures
- 4CH2 · Low-salt crystal structure of a thrombin-GpIbalpha peptide complex · the same entry in another collection · chain C against C, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain D against A, TM-score 0.92
- P07359 · AlphaFold monomer V2.0 prediction for platelet glycoprotein ib alpha chain (P07359) · a predicted model of the same protein · chain Q against A, TM-score 0.54
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 4CH2 · PDBe 4CH2 · UniProt P00734 · UniProt P07359
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