MolNFT v1 · #82777 · protein
Human alpha-thrombin-bivalirudin complex at PD5.0
3VXE · Thrombin light chain: “Human alpha-thrombin-bivalirudin complex at PD5.0”. X-ray diffraction, 1 ligand (NAG), 2 pockets (best druggability 0.31). MolNFT v1 #82777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3VXE
- Type
- protein
- Length
- 297 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin light chain; Thrombin heavy chain; Bivalirudin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG
- Pockets
- 2 · best druggability 0.31
Structure
x-ray diffraction · 4 distinct chains · 16% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 33% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 15% helix, 35% strand | P00734 |
| J | Bivalirudin | protein | 10 | 0% helix, 0% strand | — |
| I | Bivalirudin | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.31 | 0.75 | 14 | empty |
| 2 | 76 | 0.30 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1096 Ų buried · 25 hydrogen bonds · protein-protein
- H–J · 596 Ų buried · 5 hydrogen bonds · protein-protein
- H–I · 453 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 d-amino, 1 glycan (disulfide, D-amino acid, N-glycosylation).
Compared structures
- 3VXE · Human alpha-thrombin-Bivalirudin complex at PD5.0 · the same entry in another collection · chain L against L, 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 3VXE · PDBe 3VXE · UniProt P00734
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