MolNFT v1 · #11744 · protein
Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an exogenous tetrapeptide
1JVQ · Antithrombin-III: “Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive loop peptide, and an…”. X-ray diffraction, 4 ligands (ACE, NDG, NAG), 9 pockets (best druggability 0.78). MolNFT v1 #11744…
- PDB
- 1JVQ
- Type
- protein
- Length
- 827 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III; P14-P8 reactive loop peptide; Exogenous cholecystokinin tetrapeptide
- UniProt
- P01008
- Ligands
- ACE, NDG, NAG, NH2
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Antithrombin-III | protein | 406 | 30% helix, 32% strand | P01008 |
| I | Antithrombin-III | protein | 410 | 30% helix, 30% strand | P01008 |
| C | P14-P8 reactive loop peptide | protein | 7 | 0% helix, 71% strand | — |
| D | Exogenous cholecystokinin tetrapeptide | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains I, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 7 copies · chains L, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains I
- NH2 · Amino group · ion · chains I, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.78 | 0.84 | 75 | empty |
| 2 | 238 | 0.57 | 0.79 | 34 | empty |
| 3 | 91 | 0.54 | 0.84 | 22 | empty |
| 4 | 120 | 0.48 | 0.79 | 20 | empty |
| 5 | 58 | 0.46 | 0.84 | 18 | empty |
Interfaces
4 interfaces between chains.
- L–I · 1017 Ų buried · 16 hydrogen bonds · protein-protein
- I–C · 723 Ų buried · 25 hydrogen bonds · protein-protein
- I–D · 597 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 70 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1JVQ · Crystal structure at 2.6A of the ternary complex between antithrombin, a P14-P8 reactive… · 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 0.92
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 P01008
- Elsewhere: RCSB PDB 1JVQ · PDBe 1JVQ · UniProt P01008
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