4DIH
X-ray structure of the complex between human alpha thrombin and thrombin binding aptamer in the presence of sodium ions
- PDB DOI: https://doi.org/10.2210/pdb4DIH/pdb
- NAKB: 4DIH
- Classification: HYDROLASE/HYDROLASE INHIBITOR/DNA
- Organism(s): Homo sapiens, synthetic construct
- Mutation(s): No 
- Deposited: 2012-01-31 Released: 2012-07-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213 
- R-Value Work: 0.167 
- R-Value Observed: 0.186 
This is version 1.4 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Prothrombin | A [auth L] | 36 | Homo sapiens | Mutation(s): 0  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Prothrombin | B [auth H] | 259 | Homo sapiens | Mutation(s): 0  EC: 3.4.21.5 | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734 | |||||
PHAROS:  P00734 GTEx:  ENSG00000180210  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P00734 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar nucleic acids by: Sequence | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | Organism | Image | |
Thrombin binding aptamer | C [auth D] | 15 | synthetic construct | ||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
0G6 Query on 0G6 | E [auth H] | D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O | |||
NAG Query on NAG | F [auth H] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | D [auth L], H, I [auth H] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CL Query on CL | J [auth H], K [auth H] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on NA | G [auth H], L [auth D] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 5 | |||||
---|---|---|---|---|---|
ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
PRD_000020 (0G6) Query on PRD_000020 | E [auth H] | D-Phe-Pro-Arg-CH2Cl | Peptide-like / Inhibitor |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.213 
- R-Value Work: 0.167 
- R-Value Observed: 0.186 
- Space Group: P 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 43.018 | α = 65.22 |
b = 44.716 | β = 85.33 |
c = 52.689 | γ = 69.97 |
Software Name | Purpose |
---|---|
CrystalClear | data collection |
CNS | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2012-07-18  Deposition Author(s): Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.
Revision History (Full details and data files)
- Version 1.0: 2012-07-18
Type: Initial release - Version 1.1: 2012-09-26
Changes: Database references - Version 1.2: 2013-02-27
Changes: Other - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary - Version 1.4: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary