Research workbench
Crystal structure of human alpha thrombin in complex with a 27-mer aptamer bound to exosite II
Analyse Crystal structure of human alpha thrombin in complex with a 27-mer aptamer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I7Y
- Type
- protein + DNA
- Length
- 304 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; DNA (27-mer)
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, NA
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 17% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Prothrombin (EC 3.4.21.5) | protein | 250 | 15% helix, 35% strand | P00734 |
| L | Prothrombin (EC 3.4.21.5) | protein | 27 | 41% helix, 0% strand | P00734 |
| D | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- 0G6 · D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide · ligand · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains H
- NA · Sodium ion · metal · chains H
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 | 365 | 0.56 | 0.75 | 29 | empty |
| 2 | 166 | 0.51 | 0.78 | 31 | 0G6 |
| 3 | 137 | 0.49 | 0.79 | 20 | empty |
| 4 | 85 | 0.31 | 0.73 | 17 | empty |
| 5 | 63 | 0.31 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- H–D · 1115 Ų buried · 23 hydrogen bonds · protein-nucleic
- H–L · 1096 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 4I7Y · Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to… · the same entry in another collection · chain H against H, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain H 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 P00734
- Elsewhere: RCSB PDB 4I7Y · PDBe 4I7Y · UniProt P00734
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