Research workbench
X/N joint refinement of human alpha-thrombin-bivalirudin complex PD5
Analyse X/N joint refinement of human alpha-thrombin-bivalirudin complex PD5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3VXF
- Type
- protein
- Length
- 297 residues
- Chains
- 4
- Method
- x-ray diffraction; neutron 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
- 3 · best druggability 0.33
Structure
x-ray diffraction; neutron diffraction · 4 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin light chain (EC 3.4.21.5) | protein | 27 | 37% helix, 0% strand | P00734 |
| H | Thrombin heavy chain (EC 3.4.21.5) | protein | 257 | 15% helix, 34% 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
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.33 | 0.73 | 20 | empty |
| 2 | 60 | 0.33 | 0.76 | 18 | empty |
| 3 | 51 | 0.26 | 0.74 | 12 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1137 Ų buried · 24 hydrogen bonds · protein-protein
- H–J · 549 Ų buried · 3 hydrogen bonds · protein-protein
- H–I · 466 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 d-amino, 1 glycan (disulfide, D-amino acid, N-glycosylation).
Compared structures
- 3VXF · X/N Joint refinement of Human alpha-thrombin-Bivalirudin complex PD5 · 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 3VXF · PDBe 3VXF · UniProt P00734
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