- FASTA Sequence
- PDBx/mmCIF Format
- PDBx/mmCIF Format (gz)
- BinaryCIF Format (gz)
- Legacy PDB Format
- Legacy PDB Format (gz)
- PDBML/XML Format (gz)
- Structure Factors (CIF)
- Structure Factors (CIF - gz)
- Validation Full (PDF - gz)
- Validation (XML - gz)
- Validation (CIF - gz)
- Validation 2fo-fc coefficients (CIF - gz)
- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
3TK6|pdb_00003tk6
factor Xa in complex with D46-5241
- PDB DOI: https://doi.org/10.2210/pdb3TK6/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2011-08-25 Released: 2012-08-29
- Deposition Author(s): Suzuki, M.,Mochizuki, A.,Nagata, T.,Takano, H.,Kanno, H.,Kishida, M.,Ohta, T.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.241 (Depositor), 0.225 (DCC)
- R-Value Work: 0.203 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.205 (Depositor)
This is version 1.2 of the entry. See complete history.
Literature
Download MendeleyZwitter ionic potent durable orally active Factor Xa inhibitor.
Mochizuki, A., Nagata, T., Takano, H., Kanno, H., Kishida, M., Suzuki, M., Ohta, T.To be published.
Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (D46)
Global Symmetry: Asymmetric - C1
Global Stoichiometry: Hetero 2-mer - A1B1
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 32.72 kDa
- Atom Count: 2,445
- Modeled Residue Count: 287
- Deposited Residue Count: 287
- Unique protein chains: 2
Macromolecules
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Factor X heavy chain | 233 | Homo sapiens | Mutation(s): 0 EC: 3.4.21.6 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742 | |||||
PHAROS: P00742 GTEx: ENSG00000126218 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00742 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Factor X light chain | 54 | Homo sapiens | Mutation(s): 0 EC: 3.4.21.6 |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P00742 (Homo sapiens) Explore P00742 Go to UniProtKB: P00742 | |||||
PHAROS: P00742 GTEx: ENSG00000126218 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P00742 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| D46 Query on D46 Download Ideal Coordinates CCD File | E [auth A] | N-[2-({[(5-chlorothiophen-2-yl)carbonyl]amino}methyl)phenyl]-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide C20 H19 Cl N4 O2 S2 LMUFNFLXBDOGET-UHFFFAOYSA-N |  | ||
| CA Query on CA Download Ideal Coordinates CCD File | C [auth A], D [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.80 Å
- R-Value Free: 0.241 (Depositor), 0.225 (DCC)
- R-Value Work: 0.203 (Depositor), 0.192 (DCC)
- R-Value Observed: 0.205 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 56.466 | α = 90 |
| b = 72.412 | β = 90 |
| c = 79.074 | γ = 90 |
| Software Name | Purpose |
|---|---|
| manufacturer | data collection |
| REFMAC | refinement |
| CrystalClear | data reduction |
| CrystalClear | data scaling |
| REFMAC | phasing |
Entry History
Deposition Data
- Released Date: 2012-08-29 Deposition Author(s): Suzuki, M.,Mochizuki, A.,Nagata, T.,Takano, H.,Kanno, H.,Kishida, M.,Ohta, T.
Revision History (Full details and data files)
- Version 1.0: 2012-08-29
Type: Initial release - Version 1.1: 2017-11-08
Changes: Refinement description - Version 1.2: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary
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