- PDB-4d1p: Structure of human endothelial nitric oxide synthase heme domain ... -
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Basic information
Entry
Database: PDB / ID: 4d1p
Title
Structure of human endothelial nitric oxide synthase heme domain IN COMPLEX WITH 6-((((3S, 5R)-5-(((6-AMINO-4-METHYLPYRIDIN-2-YL)METHOXY) METHYL)PYRROLIDIN-3-YL)OXY) METHYL)-4-METHYLPYRIDIN-2-AMINE
Components
NITRIC OXIDE SYNTHASE, ENDOTHELIAL
Keywords
OXIDOREDUCTASE / NITRIC OXIDE SYNTHASE
Function / homology
Function and homology information
regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development ...regulation of the force of heart contraction by chemical signal / NOSIP mediated eNOS trafficking / NOSTRIN mediated eNOS trafficking / negative regulation of muscle hyperplasia / regulation of nervous system process / smooth muscle hyperplasia / response to fluid shear stress / ovulation from ovarian follicle / pulmonary valve morphogenesis / negative regulation of biomineral tissue development / positive regulation of guanylate cyclase activity / Nitric oxide stimulates guanylate cyclase / regulation of systemic arterial blood pressure by endothelin / ROS and RNS production in phagocytes / tetrahydrobiopterin binding / aortic valve morphogenesis / arginine binding / endocardial cushion morphogenesis / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / cadmium ion binding / negative regulation of potassium ion transport / negative regulation of calcium ion transport / actin monomer binding / negative regulation of platelet activation / endothelial cell migration / nitric-oxide synthase (NADPH) / positive regulation of blood vessel endothelial cell migration / blood vessel remodeling / nitric-oxide synthase activity / eNOS activation / arginine catabolic process / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / regulation of sodium ion transport / nitric oxide mediated signal transduction / Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation / homeostasis of number of cells within a tissue / lipopolysaccharide-mediated signaling pathway / nitric oxide biosynthetic process / negative regulation of blood pressure / blood vessel diameter maintenance / removal of superoxide radicals / mitochondrion organization / VEGFR2 mediated vascular permeability / cell redox homeostasis / response to hormone / caveola / establishment of localization in cell / negative regulation of smooth muscle cell proliferation / lung development / potassium ion transport / regulation of blood pressure / vasodilation / positive regulation of angiogenesis / calcium ion transport / endocytic vesicle membrane / FMN binding / NADP binding / flavin adenine dinucleotide binding / response to heat / scaffold protein binding / angiogenesis / in utero embryonic development / response to lipopolysaccharide / Extra-nuclear estrogen signaling / cytoskeleton / calmodulin binding / negative regulation of cell population proliferation / Golgi membrane / heme binding / positive regulation of gene expression / Golgi apparatus / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function
Resolution: 1.731→48.357 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 17.69 / Stereochemistry target values: ML Details: RESIDUES 110-118 IN CHAIN A AND 107-118 IN CHAIN B ARE DISORDERED
Rfactor
Num. reflection
% reflection
Rfree
0.1865
5493
5 %
Rwork
0.1566
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-
obs
0.158
109491
98.7 %
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement step
Cycle: LAST / Resolution: 1.731→48.357 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
6409
0
253
754
7416
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.007
6947
X-RAY DIFFRACTION
f_angle_d
1.19
9548
X-RAY DIFFRACTION
f_dihedral_angle_d
15.477
2533
X-RAY DIFFRACTION
f_chiral_restr
0.071
983
X-RAY DIFFRACTION
f_plane_restr
0.005
1217
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
1.7305-1.7502
0.3505
121
0.3099
2109
X-RAY DIFFRACTION
61
1.7502-1.7708
0.3464
211
0.3028
3444
X-RAY DIFFRACTION
100
1.7708-1.7924
0.3219
204
0.2668
3433
X-RAY DIFFRACTION
100
1.7924-1.8151
0.2912
188
0.2467
3458
X-RAY DIFFRACTION
100
1.8151-1.839
0.275
172
0.2286
3514
X-RAY DIFFRACTION
100
1.839-1.8642
0.2643
169
0.2079
3478
X-RAY DIFFRACTION
100
1.8642-1.8908
0.2322
188
0.1924
3491
X-RAY DIFFRACTION
100
1.8908-1.919
0.2331
188
0.1912
3453
X-RAY DIFFRACTION
100
1.919-1.949
0.2334
214
0.1784
3466
X-RAY DIFFRACTION
100
1.949-1.981
0.244
183
0.1659
3447
X-RAY DIFFRACTION
100
1.981-2.0151
0.1729
178
0.1627
3520
X-RAY DIFFRACTION
100
2.0151-2.0518
0.2058
193
0.1602
3429
X-RAY DIFFRACTION
100
2.0518-2.0912
0.2025
182
0.1609
3505
X-RAY DIFFRACTION
100
2.0912-2.1339
0.174
180
0.1576
3484
X-RAY DIFFRACTION
100
2.1339-2.1803
0.2053
206
0.1569
3472
X-RAY DIFFRACTION
100
2.1803-2.231
0.195
177
0.1546
3514
X-RAY DIFFRACTION
100
2.231-2.2868
0.1858
171
0.1511
3475
X-RAY DIFFRACTION
100
2.2868-2.3486
0.1924
188
0.1503
3518
X-RAY DIFFRACTION
100
2.3486-2.4178
0.2063
175
0.1526
3487
X-RAY DIFFRACTION
100
2.4178-2.4958
0.21
176
0.1531
3548
X-RAY DIFFRACTION
100
2.4958-2.585
0.1725
177
0.1518
3522
X-RAY DIFFRACTION
100
2.585-2.6885
0.1799
192
0.1528
3502
X-RAY DIFFRACTION
100
2.6885-2.8108
0.1962
183
0.1498
3518
X-RAY DIFFRACTION
100
2.8108-2.959
0.1944
188
0.1558
3550
X-RAY DIFFRACTION
100
2.959-3.1444
0.1815
155
0.1564
3559
X-RAY DIFFRACTION
100
3.1444-3.3871
0.1702
204
0.1509
3497
X-RAY DIFFRACTION
100
3.3871-3.7278
0.1852
175
0.1403
3590
X-RAY DIFFRACTION
100
3.7278-4.267
0.1498
184
0.1252
3589
X-RAY DIFFRACTION
100
4.267-5.3748
0.128
192
0.1235
3626
X-RAY DIFFRACTION
100
5.3748-48.3756
0.1743
179
0.1772
3800
X-RAY DIFFRACTION
100
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
0.1013
0.012
-0.0851
0.4786
-0.1146
0.6447
0.0218
0.0024
0.0551
0.1237
-0.0036
0.0341
-0.0606
-0.0369
-0
0.1435
0.0076
0.0041
0.1326
-0.0136
0.1309
17.0059
243.125
32.192
2
0.1282
0.1392
-0.1069
0.7934
-0.2007
0.2954
-0.0001
-0.0009
-0.0005
-0.117
-0.0575
-0.0565
0.0825
0.0136
-0.0604
0.0698
-0.0047
0.0147
0.0817
0.0109
0.0768
30.0793
215.8017
9.9356
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
(CHAINAANDRESID67:480)
2
X-RAY DIFFRACTION
2
(CHAINBANDRESID67:480)
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