Research workbench
2.5A crystal structure of the antithrombin-thrombin-heparin ternary complex
Analyse 2.5A crystal structure of the antithrombin-thrombin-heparin ternary complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1TB6
- Type
- protein
- Length
- 714 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thrombin; Antithrombin-III
- EC
- 3.4.21.5
- UniProt
- P00734, P01008
- Ligands
- GU8, GU9, GU6, GU5, GU3, GU2, GU1, GU0, GU4, NAG, BMA, MAN, FUC
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Thrombin | protein | 43 | 30% helix, 0% strand | P00734 |
| H | Thrombin (EC 3.4.21.5) | protein | 259 | 15% helix, 32% strand | P00734 |
| I | Antithrombin-III | protein | 412 | 30% helix, 27% strand | P01008 |
Ligands and binding sites
- GU8 · 2,3,6-tri-O-methyl-beta-D-glucopyranose · ligand · 4 copies · chains I
- GU9 · 2,3,6-tri-O-methyl-alpha-D-glucopyranose · ligand · 3 copies
- GU6 · 2,3,6-tri-O-sulfo-alpha-D-glucopyranose · ligand · 2 copies · chains I, H
- GU5 · 2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose · ligand · 2 copies · chains I
- GU3 · methyl 3-O-methyl-2,6-di-O-sulfo-alpha-D-glucopyranoside · ligand · chains I
- GU2 · 2,3-di-O-methyl-alpha-L-idopyranuronic acid · ligand · chains I
- GU1 · 2,3-di-O-methyl-beta-D-glucopyranuronic acid · ligand · chains I
- GU0 · 2,3,6-tri-O-sulfonato-beta-D-glucopyranose · ligand · chains H
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains H, I
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains I
- FUC · alpha-L-fucopyranose · sugar
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 8 copies · chains H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.78 | 0.84 | 72 | MPD |
| 2 | 167 | 0.67 | 0.86 | 34 | MPD |
| 3 | 229 | 0.62 | 0.82 | 29 | MPD |
| 4 | 146 | 0.47 | 0.77 | 23 | empty |
| 5 | 56 | 0.33 | 0.78 | 18 | empty |
Interfaces
2 interfaces between chains.
- L–H · 1743 Ų buried · 29 hydrogen bonds · protein-protein
- H–I · 1437 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1TB6 · 2.5A Crystal Structure of the Antithrombin-Thrombin-Heparin Ternary Complex · the same entry in another collection · chain L against L, TM-score 1.00
- P01008 · AlphaFold monomer V2.0 prediction for antithrombin-III (P01008) · a predicted model of the same protein · chain I against A, TM-score 0.97
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 P01008
- Elsewhere: RCSB PDB 1TB6 · PDBe 1TB6 · UniProt P00734 · UniProt P01008
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