MolNFT v1 · #21972 · protein
Antithrombin-anhydrothrombin-heparin ternary complex structure
1SR5 · Antithrombin-III: “Antithrombin-anhydrothrombin-heparin ternary complex structure”. X-ray diffraction, 9 ligands (YYB, U9J, GU6), 6 pockets (best druggability 0.67). MolNFT v1 #21972 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1SR5
- Type
- protein
- Length
- 689 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antithrombin-III; Prothrombin
- EC
- 3.4.21.5
- UniProt
- P01008, P00734
- Ligands
- YYB, U9J, GU6, U9M, U9G, GU8, U9D, GU4, NAG
- Pockets
- 6 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Antithrombin-III | protein | 409 | 28% helix, 25% strand | P01008 |
| B | Prothrombin (EC 3.4.21.5) | protein | 32 | 25% helix, 0% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 248 | 13% helix, 32% strand | P00734 |
Ligands and binding sites
- YYB · 1,5-anhydro-3-O-methyl-2,6-di-O-sulfo-D-glucitol · ligand · chains A
- U9J · (2R,3R,4S,5S,6R)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol · ligand · chains A
- GU6 · 2,3,6-tri-O-sulfo-alpha-D-glucopyranose · ligand · chains A
- U9M · (2R,3R,4S,5S,6S)-6-(dihydroxymethyl)-3,4-dimethoxytetrahydro-2H-pyran-2,5-diol · ligand · chains A
- U9G · 2,3-di-O-methyl-6-O-sulfo-alpha-D-glucopyranose · ligand · chains A
- GU8 · 2,3,6-tri-O-methyl-beta-D-glucopyranose · ligand · chains A
- U9D · 4-deoxy-2,3,6-tri-O-methyl-alpha-D-xylo-hexopyranose · ligand
- GU4 · 2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose · ligand · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 469 | 0.67 | 0.79 | 51 | empty |
| 2 | 137 | 0.46 | 0.77 | 20 | empty |
| 3 | 76 | 0.45 | 0.81 | 20 | empty |
| 4 | 56 | 0.38 | 0.80 | 17 | empty |
| 5 | 57 | 0.33 | 0.77 | 17 | empty |
Interfaces
2 interfaces between chains.
- B–C · 1321 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 962 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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
- Every structure of UniProt P00734
- Elsewhere: RCSB PDB 1SR5 · PDBe 1SR5 · UniProt P01008 · UniProt P00734
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