MolNFT v1 · #89569 · protein
Crystal structure of thrombin bound to the activation domain qedqvdprlidgkmtrrgds of protein C
4DT7 · Thrombin light chain: “Crystal structure of thrombin bound to the activation domain qedqvdprlidgkmtrrgds of protein C”. X-ray diffraction, 1 ligand (NA), 9 pockets (best druggability 0.58). MolNFT v1 #89569 on GenesisL1: 3D…
- PDB
- 4DT7
- Type
- protein
- Length
- 586 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Vitamin K-dependent protein C
- EC
- 3.4.21.5, 3.4.21.69
- UniProt
- P00734, P04070
- Ligands
- NA
- Pockets
- 9 · best druggability 0.58
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Thrombin light chain (EC 3.4.21.5) | protein | 32 | 38% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 252 | 16% helix, 35% strand | P00734 |
| D | Thrombin heavy chain (EC 3.4.21.5) | protein | 253 | 15% helix, 34% strand | P00734 |
| E | Vitamin K-dependent protein C (EC 3.4.21.69) | protein | 8 | 0% helix, 25% strand | P04070 |
| F | Vitamin K-dependent protein C (EC 3.4.21.69) | protein | 9 | 0% helix, 22% strand | P04070 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
- ACT · Acetate ion · additive · 2 copies · chains B, D
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.58 | 0.85 | 33 | ACT |
| 2 | 121 | 0.41 | 0.76 | 17 | empty |
| 3 | 130 | 0.41 | 0.75 | 17 | empty |
| 4 | 112 | 0.41 | 0.76 | 16 | empty |
| 5 | 119 | 0.39 | 0.74 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1208 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1166 Ų buried · 29 hydrogen bonds · protein-protein
- D–F · 717 Ų buried · 20 hydrogen bonds · protein-protein
- B–E · 620 Ų buried · 18 hydrogen bonds · protein-protein
- B–D · 447 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4DT7 · Crystal structure of thrombin bound to the activation domain QEDQVDPRLIDGKMTRRGDS of… · the same entry in another collection · chain F against F, TM-score 1.00
- P04070 · AlphaFold monomer V2.0 prediction for vitamin K-dependent protein C (P04070) · a predicted model of the same protein · chain E against A, TM-score 0.37
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 P04070
- Elsewhere: RCSB PDB 4DT7 · PDBe 4DT7 · UniProt P00734 · UniProt P04070
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