4I7Y
Crystal Structure of Human Alpha Thrombin in Complex with a 27-mer Aptamer Bound to Exosite II
- PDB DOI: https://doi.org/10.2210/pdb4I7Y/pdb
- NAKB: 4I7Y
- Classification: HYDROLASE/HYDROLASE INHIBITOR/DNA
- Organism(s): Homo sapiens, synthetic construct
- Mutation(s): No
- Deposited: 2012-12-01 Released: 2013-10-16
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.249
- R-Value Work: 0.181
- R-Value Observed: 0.184
This is version 1.3 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 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 | |||||
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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 L] | 36 | 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:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Length | Organism | Image | |
| DNA (27-MER) | C [auth D] | 27 | synthetic construct |  | |
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| 0G6 Query on 0G6 | D [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 L] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |  | ||
| NA Query on NA | E [auth H] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4 | |||||
|---|---|---|---|---|---|
| ID | Chains | Name | Type/Class | 2D Diagram | 3D Interactions |
| PRD_000020 (0G6) Query on PRD_000020 | D [auth H] | D-Phe-Pro-Arg-CH2Cl | Peptide-like / Inhibitor | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.249
- R-Value Work: 0.181
- R-Value Observed: 0.184
- Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 48.144 | α = 90 |
| b = 81.904 | β = 99.66 |
| c = 53.72 | γ = 90 |
| Software Name | Purpose |
|---|---|
| DENZO | data reduction |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2013-10-16 Deposition Author(s): Pica, A., Russo Krauss, I., Merlino, A., Mazzarella, L., Sica, F.
Revision History (Full details and data files)
- Version 1.0: 2013-10-16
Type: Initial release - Version 1.1: 2013-12-11
Changes: Database references - Version 1.2: 2014-01-01
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
