MolNFT v1 · #31779 · protein
2.1 ångström structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781 and two S195A thrombin molecules
2B5T: “2.1 ångström structure of a nonproductive complex between antithrombin, synthetic heparin mimetic SR123781…”. X-ray diffraction, 14 ligands (GU8, GU9, GU6), 8 pockets (best druggability 0.57). MolNFT v1 #31779 on GenesisL1: 3D…
- PDB
- 2B5T
- Type
- protein
- Length
- 1,012 residues
- Chains
- 5
- 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, FUC, MAN, BMA, SO4
- Pockets
- 8 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thrombin | protein | 47 | 28% helix, 0% strand | P00734 |
| B, D | Thrombin (EC 3.4.21.5) | protein | 252 | 15% helix, 35% strand | P00734 |
| C | Thrombin | protein | 46 | 26% helix, 0% strand | P00734 |
| I | Antithrombin-III | protein | 415 | 30% helix, 26% 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, B, D
- GU5 · 2,3-di-O-methyl-6-O-sulfonato-alpha-D-glucopyranose · ligand · 2 copies · chains I, B, D
- 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 B, D
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains B, D, I
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains I
- MAN · alpha-D-mannopyranose · sugar · 3 copies
- BMA · beta-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 6 copies · chains B, D, I
- GOL · Glycerol · additive · 12 copies · chains A, B, D, C, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.57 | 0.74 | 33 | GU6, GU4 |
| 2 | 222 | 0.54 | 0.78 | 40 | empty |
| 3 | 220 | 0.54 | 0.77 | 39 | empty |
| 4 | 149 | 0.50 | 0.78 | 20 | empty |
| 5 | 91 | 0.49 | 0.82 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1820 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 1776 Ų buried · 41 hydrogen bonds · protein-protein
- B–D · 80 Ų buried · 1 hydrogen bond · protein-protein
- A–I · 69 Ų buried · 4 hydrogen bonds · protein-protein
- B–I · 53 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 2B5T · 2.1 Angstrom structure of a nonproductive complex between antithrombin, synthetic heparin… · the same entry in another collection · chain A against A, 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 0.91
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 2B5T · PDBe 2B5T · UniProt P00734 · UniProt P01008
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