MolNFT v1 · #123236 · protein
Crystal structure for human thrombin mutant D189A
5JDU · Thrombin light chain: “Crystal structure for human thrombin mutant D189A”. X-ray diffraction, 2 ligands (NAG, CL), 8 pockets (best druggability 0.70). MolNFT v1 #123236 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5JDU
- Type
- protein
- Length
- 551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin light chain (EC 3.4.21.5) | protein | 30 | 30% helix, 0% strand | P00734 |
| B | Thrombin heavy chain (EC 3.4.21.5) | protein | 245 | 16% helix, 36% strand | P00734 |
| C | Thrombin light chain (EC 3.4.21.5) | protein | 29 | 31% helix, 0% strand | P00734 |
| D | Thrombin heavy chain (EC 3.4.21.5) | protein | 247 | 17% helix, 35% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, D
- CL · Chloride ion · ion · chains D
- GOL · Glycerol · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 54 | 0.70 | 0.97 | 22 | CL |
| 2 | 181 | 0.48 | 0.76 | 35 | empty |
| 3 | 144 | 0.46 | 0.76 | 37 | empty |
| 4 | 88 | 0.45 | 0.80 | 23 | empty |
| 5 | 81 | 0.44 | 0.80 | 23 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1249 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 1136 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 160 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5JDU · Crystal structure for human thrombin mutant D189A · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 5JDU · PDBe 5JDU · UniProt P00734
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