- PDB-5k0h: Human factor Xa in complex with synthetic inhibitor benzylsulfony... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 5k0h
Title
Human factor Xa in complex with synthetic inhibitor benzylsulfonyl-dSer(Benzyl)-Gly-4-amidinobenzylamide
Components
(Coagulation factor XFactor X) x 2
Keywords
HYDROLASE / human factor Xa / inhibitor complex / benzamidine inhibitor / clotting factor
Function / homology
Function and homology information
coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function
CoagulationfactorX / Factor X / Stuart factor / Stuart-Prower factor
Mass: 26447.104 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein
CoagulationfactorX / Factor X / Stuart factor / Stuart-Prower factor
Mass: 5460.055 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
Resolution: 2.2→19.25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1177536.28 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.261
1631
10.1 %
RANDOM
Rwork
0.214
-
-
-
obs
0.214
16160
97.6 %
-
Solvent computation
Bsol: 41.5057 Å2 / ksol: 0.339348 e/Å3
Displacement parameters
Biso mean: 47.6 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-7.87 Å2
0 Å2
0 Å2
2-
-
-15.71 Å2
0 Å2
3-
-
-
23.58 Å2
Refine analyze
Free
Obs
Luzzati coordinate error
0.35 Å
0.28 Å
Luzzati d res low
-
5 Å
Luzzati sigma a
0.39 Å
0.32 Å
Refinement step
Cycle: 1 / Resolution: 2.2→19.25 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2229
0
40
143
2412
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.006
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.2
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
24.4
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
0.74
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
1.6
1.5
X-RAY DIFFRACTION
c_mcangle_it
2.68
2
X-RAY DIFFRACTION
c_scbond_it
2.1
2
X-RAY DIFFRACTION
c_scangle_it
3.2
2.5
LS refinement shell
Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
Rfactor
Num. reflection
% reflection
Rfree
0.332
263
10 %
Rwork
0.306
2356
-
obs
-
-
97 %
Xplor file
Refine-ID
Serial no
Param file
Topol file
X-RAY DIFFRACTION
1
MSI_CNX_TOPPAR/protein_rep.param
MSI_CNX_TOPPAR/protein.top
X-RAY DIFFRACTION
2
MSI_CNX_TOPPAR/water_rep.param
MSI_CNX_TOPPAR/water.top
X-RAY DIFFRACTION
3
MSI_CNX_TOPPAR/ion.param
MSI_CNX_TOPPAR/ion.top
X-RAY DIFFRACTION
4
../../../inh/cu1/inh.par
../../../inh/cu1/inh.top
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