Research workbench
X-ray structure of the complex between human alpha thrombin and two DUPLEX/QUADRUPLEX aptamers: NU172 and HD22_27MER
Analyse X-ray structure of the complex between human alpha thrombin and two… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7NTU
- Type
- protein + DNA
- Length
- 660 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prothrombin; NU172; HD22_27MER
- EC
- 3.4.21.5
- UniProt
- P00734
- Ligands
- 0G6, NAG, NA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Prothrombin (EC 3.4.21.5) | protein | 28 | 29% helix, 0% strand | P00734 |
| B, D | Prothrombin (EC 3.4.21.5) | protein | 249 | 15% helix, 35% strand | P00734 |
| E, G | NU172 | dna | 26 | — | — |
| F, I | HD22_27MER | 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 · 2 copies · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, D
- NA · Sodium ion · metal · 4 copies · chains E, F, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.83 | 0.85 | 77 | empty |
| 2 | 349 | 0.58 | 0.77 | 28 | empty |
| 3 | 354 | 0.56 | 0.76 | 28 | empty |
| 4 | 241 | 0.56 | 0.78 | 41 | 0G6 |
| 5 | 206 | 0.56 | 0.79 | 37 | 0G6 |
Interfaces
8 interfaces between chains.
- A–B · 1158 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1149 Ų buried · 24 hydrogen bonds · protein-protein
- D–I · 1140 Ų buried · 26 hydrogen bonds · protein-nucleic
- B–F · 1121 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–E · 603 Ų buried · 18 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 2 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 7NTU · X-ray structure of the complex between human alpha thrombin and two duplex/quadruplex… · the same entry in another collection · chain I against I, TM-score 1.00
- P00734 · AlphaFold monomer V2.0 prediction for prothrombin (P00734) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 7NTU · PDBe 7NTU · UniProt P00734
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