MolNFT v1 · #76218 · protein
Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4.
3QDZ · Thrombin light chain: “Crystal structure of the human thrombin mutant D102N in complex with the extracellular fragment of human PAR4.”. X-ray diffraction, 5 pockets (best druggability 0.73). MolNFT v1 #76218 on GenesisL1: 3D…
- PDB
- 3QDZ
- Type
- protein
- Length
- 579 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Proteinase-activated receptor 4
- EC
- 3.4.21.5
- UniProt
- P00734, Q96RI0
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 17% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 251 | 13% helix, 32% strand | P00734 |
| D | Thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 11% helix, 30% strand | P00734 |
| E | Proteinase-activated receptor 4 | protein | 9 | 0% helix, 33% strand | Q96RI0 |
| F | Proteinase-activated receptor 4 | protein | 4 | 0% helix, 25% strand | Q96RI0 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 832 | 0.73 | 0.78 | 68 | empty |
| 2 | 59 | 0.61 | 0.91 | 22 | empty |
| 3 | 53 | 0.54 | 0.89 | 17 | empty |
| 4 | 79 | 0.32 | 0.74 | 16 | empty |
| 5 | 63 | 0.32 | 0.76 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1190 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1184 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 540 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 461 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 445 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3QDZ · Crystal structure of the human thrombin mutant D102N in complex with the extracellular… · the same entry in another collection · chain F against F, TM-score 1.00
- Q96RI0 · AlphaFold monomer V2.0 prediction for proteinase-activated receptor 4 (Q96RI0) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 Q96RI0
- Elsewhere: RCSB PDB 3QDZ · PDBe 3QDZ · UniProt P00734 · UniProt Q96RI0
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