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Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an exogenous tripeptide
Analyse Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LK6
- Type
- protein
- Length
- 825 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III; Antithrombin P14-P9 peptide; Exogenous tripeptide formyl-mlf
- UniProt
- P01008
- Ligands
- ACE, NDG, NAG
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 31% 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 | 32% helix, 30% strand | P01008 |
| C | Antithrombin P14-P9 peptide | protein | 6 | 0% helix, 67% strand | — |
| D | Exogenous tripeptide formyl-mlf | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains I, C
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 6 copies · chains L, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains I
- GOL · Glycerol · additive · chains I, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.77 | 0.83 | 69 | empty |
| 2 | 196 | 0.53 | 0.78 | 30 | empty |
| 3 | 172 | 0.49 | 0.77 | 22 | empty |
| 4 | 156 | 0.49 | 0.78 | 33 | empty |
| 5 | 62 | 0.37 | 0.78 | 14 | empty |
Interfaces
4 interfaces between chains.
- L–I · 1008 Ų buried · 14 hydrogen bonds · protein-protein
- I–C · 627 Ų buried · 19 hydrogen bonds · protein-protein
- I–D · 488 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 11 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, formylation).
Compared structures
- 1LK6 · Structure of dimeric antithrombin complexed with a P14-P9 reactive loop peptide and an… · 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 1LK6 · PDBe 1LK6 · UniProt P01008
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