MolNFT v1 · #20379 · protein
2.5A structure of anticoagulant thrombin variant E217K
1RD3 · Prothrombin: “2.5A structure of anticoagulant thrombin variant E217K”. X-ray diffraction, 6 ligands (NAG, NDG, FUC), 5 pockets (best druggability 0.73). MolNFT v1 #20379 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1RD3
- Type
- protein
- Length
- 581 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- NAG, NDG, FUC, BMA, MAN, PO4
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prothrombin (EC 3.4.21.5) | protein | 33 | 36% helix, 0% strand | P00734 |
| B | Prothrombin (EC 3.4.21.5) | protein | 259 | 16% helix, 34% strand | P00734 |
| C | Prothrombin (EC 3.4.21.5) | protein | 31 | 45% helix, 0% strand | P00734 |
| D | Prothrombin (EC 3.4.21.5) | protein | 258 | 14% helix, 34% strand | P00734 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- PO4 · Phosphate ion · ion · 3 copies · chains B, D
- GOL · Glycerol · additive · 6 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.73 | 0.77 | 74 | empty |
| 2 | 242 | 0.54 | 0.77 | 31 | GOL |
| 3 | 233 | 0.54 | 0.77 | 32 | empty |
| 4 | 129 | 0.44 | 0.77 | 20 | empty |
| 5 | 53 | 0.29 | 0.75 | 12 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1323 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 1198 Ų buried · 29 hydrogen bonds · protein-protein
- B–D · 1094 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1RD3 · 2.5A Structure of Anticoagulant Thrombin Variant E217K · the same entry in another collection · chain A against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 1RD3 · PDBe 1RD3 · UniProt P00734
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