- PDB-3tzi: X-ray crystal structure of arachidonic acid bound in the cyclooxy... -
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Basic information
Entry
Database: PDB / ID: 3tzi
Title
X-ray crystal structure of arachidonic acid bound in the cyclooxygenase channel of G533V murine COX-2
Components
Prostaglandin G/H synthase 2
Keywords
OXIDOREDUCTASE / N-glycosylation / Monotopic Membrane Protein
Function / homology
Function and homology information
Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / positive regulation of fibroblast growth factor production ...Biosynthesis of DHA-derived SPMs / Biosynthesis of EPA-derived SPMs / Biosynthesis of DPAn-3 SPMs / Biosynthesis of electrophilic ω-3 PUFA oxo-derivatives / Synthesis of 15-eicosatetraenoic acid derivatives / cellular response to non-ionic osmotic stress / positive regulation of platelet-derived growth factor production / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / prostanoid biosynthetic process / regulation of neuroinflammatory response / cyclooxygenase pathway / positive regulation of prostaglandin biosynthetic process / positive regulation of fever generation / positive regulation of smooth muscle contraction / response to selenium ion / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / prostaglandin secretion / positive regulation of synaptic plasticity / cellular response to fluid shear stress / response to nematode / prostaglandin biosynthetic process / negative regulation of smooth muscle contraction / nuclear inner membrane / positive regulation of cell migration involved in sprouting angiogenesis / bone mineralization / maintenance of blood-brain barrier / decidualization / negative regulation of calcium ion transport / negative regulation of cell cycle / nuclear outer membrane / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / positive regulation of vasoconstriction / positive regulation of vascular endothelial growth factor production / keratinocyte differentiation / positive regulation of brown fat cell differentiation / positive regulation of synaptic transmission, glutamatergic / response to cytokine / embryo implantation / positive regulation of smooth muscle cell proliferation / brown fat cell differentiation / learning / peroxidase activity / positive regulation of protein import into nucleus / caveola / regulation of blood pressure / memory / positive regulation of nitric oxide biosynthetic process / regulation of cell population proliferation / response to oxidative stress / angiogenesis / response to lipopolysaccharide / cellular response to hypoxia / neuron projection / positive regulation of apoptotic process / endoplasmic reticulum lumen / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / endoplasmic reticulum / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm / cytosol Similarity search - Function
Resolution: 2.15→19.99 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.872 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2096
4039
5 %
RANDOM
Rwork
0.16976
-
-
-
obs
0.17179
76377
99.98 %
-
all
-
80417
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 29.812 Å2
Baniso -1
Baniso -2
Baniso -3
1-
1.01 Å2
0 Å2
0 Å2
2-
-
0.06 Å2
0 Å2
3-
-
-
-1.07 Å2
Refine analyze
Luzzati sigma a obs: 0.299 Å
Refinement step
Cycle: LAST / Resolution: 2.15→19.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8869
0
343
816
10028
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.01
0.022
9577
X-RAY DIFFRACTION
r_bond_other_d
X-RAY DIFFRACTION
r_angle_refined_deg
1.266
2.003
13035
X-RAY DIFFRACTION
r_angle_other_deg
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.44
5
1123
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.643
23.956
450
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
14.109
15
1495
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
11.868
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.086
0.2
1383
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.021
7392
X-RAY DIFFRACTION
r_gen_planes_other
X-RAY DIFFRACTION
r_nbd_refined
X-RAY DIFFRACTION
r_nbd_other
X-RAY DIFFRACTION
r_nbtor_refined
X-RAY DIFFRACTION
r_nbtor_other
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
X-RAY DIFFRACTION
r_xyhbond_nbd_other
X-RAY DIFFRACTION
r_metal_ion_refined
X-RAY DIFFRACTION
r_metal_ion_other
X-RAY DIFFRACTION
r_symmetry_vdw_refined
X-RAY DIFFRACTION
r_symmetry_vdw_other
X-RAY DIFFRACTION
r_symmetry_hbond_refined
X-RAY DIFFRACTION
r_symmetry_hbond_other
X-RAY DIFFRACTION
r_symmetry_metal_ion_refined
X-RAY DIFFRACTION
r_symmetry_metal_ion_other
X-RAY DIFFRACTION
r_mcbond_it
0.342
1.5
5558
X-RAY DIFFRACTION
r_mcbond_other
X-RAY DIFFRACTION
r_mcangle_it
0.665
2
9037
X-RAY DIFFRACTION
r_scbond_it
1.39
3
4019
X-RAY DIFFRACTION
r_scangle_it
2.321
4.5
3988
X-RAY DIFFRACTION
r_rigid_bond_restr
X-RAY DIFFRACTION
r_sphericity_free
X-RAY DIFFRACTION
r_sphericity_bonded
LS refinement shell
Resolution: 2.15→2.205 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.272
311
-
Rwork
0.233
5537
-
obs
-
-
99.93 %
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
1.6217
-1.2774
0.7714
4.5305
-1.52
3.4836
-0.0005
0.1763
0.0173
-0.0029
0.0645
-0.2769
-0.2803
0.5423
-0.064
0.0809
-0.0738
0.0623
0.26
-0.0674
0.2299
59.5235
38.2426
30.2784
2
1.2725
-1.2026
1.3629
20.953
1.9223
2.0375
0.4694
0.2189
-0.3329
0.0359
-0.1851
-0.2855
0.6587
0.2459
-0.2843
0.2943
0.1047
0.0932
0.4549
-0.1072
0.6084
66.8305
20.5337
28.0143
3
2.5069
-3.2744
-0.0466
5.2905
-1.7833
3.6513
-0.135
-0.1409
0.0918
-0.289
-0.0077
-0.4121
0.6239
0.4667
0.1428
0.3288
0.0492
0.2627
0.2416
-0.1777
0.6477
50.0676
5.42
17.0762
4
2.6349
-1.7249
-0.971
6.1723
2.8247
11.5997
-0.096
0.0151
-0.076
0.5371
-0.1532
-0.9455
0.5831
0.5679
0.2492
0.2712
0.1676
0.0495
0.3415
0.0038
0.4417
46.3543
3.7199
29.4641
5
1.2428
0.5505
0.0756
1.0944
0.7941
4.2987
-0.0714
0.1531
0.0413
-0.1259
0.1197
-0.1042
-0.3421
0.2759
-0.0483
0.0691
-0.0406
0.0314
0.0493
0.0001
0.0821
42.5912
37.2484
24.2988
6
1.5933
1.4112
0.3813
1.4944
0.4188
3.4689
-0.0934
0.1567
0.1381
-0.1409
0.0267
0.1669
-0.1509
-0.1741
0.0667
0.0249
0.0265
-0.0091
0.0811
0.0091
0.0729
28.5817
24.115
21.9634
7
2.8733
-0.074
1.0109
1.274
-0.239
4.1006
0.0014
0.2245
0.2152
0.0414
-0.0012
0.3005
-0.0918
-0.4521
-0.0002
0.0231
-0.0149
0.0362
0.1311
-0.0138
0.1229
12.0628
19.5628
30.7525
8
1.5544
0.7268
-0.4849
0.9164
0.1058
2.2647
-0.0404
0.1389
-0.2228
0.0022
0.0511
-0.1715
0.2821
0.0938
-0.0107
0.0662
0.0093
0.0177
0.0271
-0.0333
0.0821
31.7929
14.1626
30.1344
9
4.8527
-2.5613
1.6218
4.3263
-3.4205
5.2865
0.197
0.5608
0.0809
-0.4343
-0.16
0.2694
0.2427
-0.8341
-0.037
0.1451
-0.0271
-0.0276
0.4531
-0.0449
0.101
13.4487
16.6686
11.4404
10
2.3972
1.2547
0.936
1.8787
0.6821
2.1209
-0.1488
0.2577
0.0852
-0.207
0.1576
-0.0167
-0.1442
0.1117
-0.0087
0.1011
-0.0632
0.0451
0.1238
-0.0049
0.033
40.485
29.9763
14.4558
11
1.4072
0.8805
-0.7055
1.9208
-0.9063
3.4232
-0.1609
0.3136
-0.1665
-0.3183
0.1194
-0.2353
0.0591
0.1755
0.0415
0.0871
-0.0564
0.0587
0.1709
-0.0577
0.0952
44.6024
25.7604
12.4818
12
1.3955
0.4324
0.4949
1.9018
-0.0905
3.2634
0.0469
0.1297
-0.3478
0.0727
0.033
-0.1437
0.5358
-0.0072
-0.0799
0.1391
-0.0166
0.0353
0.0159
-0.0434
0.1265
25.9258
5.7362
32.263
13
4.6086
-0.1541
-1.762
0.6716
-0.9573
3.2543
-0.1312
-0.0387
-0.2262
0.0788
0.0246
0.0001
0.8234
-0.1545
0.1066
0.7722
-0.1181
-0.0026
0.0215
0.0193
0.2256
27.0131
2.0529
56.9502
14
6.2324
1.3318
0.7385
11.4181
6.5799
3.8407
-0.0806
0.4165
-1.3048
0.6098
1.0173
-1.7518
0.4917
0.69
-0.9367
0.6948
0.2242
-0.0601
0.3843
0.028
0.7102
45.7969
0.1364
62.0155
15
2.414
1.186
-2.3962
2.4947
-1.9399
10.2484
-0.0295
-0.3099
-0.6232
-0.0554
-0.1443
-0.4235
0.6063
0.6097
0.1738
0.2396
0.1773
-0.0937
0.2598
0.0314
0.5098
60.0036
18.971
64.1543
16
0.6495
0.2216
0.7265
1.2284
1.1308
5.3745
0.076
-0.1146
-0.0886
0.2762
-0.1383
0.0306
0.4511
-0.3643
0.0623
0.1384
-0.0637
0.0074
0.0427
0.0111
0.0861
25.8427
19.2324
63.1009
17
0.9363
0.7269
-0.906
1.9784
0.4424
1.8343
0.071
0.0415
0.089
0.0796
-0.0496
0.1409
-0.0398
-0.1693
-0.0214
0.013
-0.0099
0.0256
0.133
-0.0137
0.0709
36.7601
36.2321
61.8254
18
1.383
0.1504
-0.2814
3.6288
2.6511
5.4481
0.0122
-0.0316
0.3184
-0.3548
-0.0507
0.0183
-0.8002
-0.052
0.0385
0.1385
-0.001
0.0254
0.0056
-0.0258
0.1551
40.1947
55.4014
52.4732
19
1.3621
0.1181
-0.4291
2.0623
-0.5756
3.392
0.0565
-0.1081
0.1695
0.07
0.1151
0.0302
-0.3539
0.0309
-0.1717
0.043
-0.0091
0.021
0.0295
-0.0367
0.0842
43.7608
45.8868
56.108
20
1.35
0.3573
0.0246
1.8425
0.5562
2.3773
0.036
-0.155
-0.115
0.1921
0.0387
-0.1882
0.1547
0.2253
-0.0748
0.0487
-0.0037
-0.0424
0.0556
0.0271
0.061
44.7831
29.8957
62.5972
21
4.1424
0.1709
-2.0694
5.0157
0.3159
4.7239
0.147
-0.3119
0.2782
0.2833
0.0164
0.2246
-0.2134
0.0349
-0.1634
0.1436
-0.0755
0.0636
0.1426
-0.0748
0.0886
41.2054
50.542
74.4126
22
1.3434
0.7825
0.6935
2.6883
1.952
2.5314
0.1
-0.2189
0.0469
0.2827
-0.1086
0.1022
0.3179
-0.208
0.0086
0.1749
-0.0633
0.0134
0.1071
0.0333
0.0354
30.9614
25.2602
73.2397
23
0.8907
0.6233
-0.3822
1.202
-0.2475
1.5656
0.0839
-0.27
-0.1916
0.2196
-0.0781
-0.1113
0.4486
0.2394
-0.0058
0.2083
0.0371
-0.042
0.1156
0.0339
0.1146
39.95
20.52
68.2161
24
1.5948
0.9504
-0.8711
2.6705
0.9765
5.5231
0.0906
-0.3773
0.042
0.1826
0.1619
-0.2687
-0.0125
0.8117
-0.2524
0.0155
-0.0005
-0.0294
0.1904
-0.0802
0.1586
56.2806
42.7687
61.5522
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Auth asym-ID
Auth seq-ID
1
X-RAY DIFFRACTION
1
A
33 - 68
2
X-RAY DIFFRACTION
2
A
69 - 82
3
X-RAY DIFFRACTION
3
A
83 - 102
4
X-RAY DIFFRACTION
4
A
103 - 122
5
X-RAY DIFFRACTION
5
A
123 - 185
6
X-RAY DIFFRACTION
6
A
186 - 231
7
X-RAY DIFFRACTION
7
A
232 - 320
8
X-RAY DIFFRACTION
8
A
321 - 397
9
X-RAY DIFFRACTION
9
A
398 - 429
10
X-RAY DIFFRACTION
10
A
430 - 478
11
X-RAY DIFFRACTION
11
A
479 - 537
12
X-RAY DIFFRACTION
12
A
538 - 582
13
X-RAY DIFFRACTION
13
B
33 - 67
14
X-RAY DIFFRACTION
14
B
68 - 87
15
X-RAY DIFFRACTION
15
B
88 - 122
16
X-RAY DIFFRACTION
16
B
123 - 186
17
X-RAY DIFFRACTION
17
B
187 - 240
18
X-RAY DIFFRACTION
18
B
241 - 268
19
X-RAY DIFFRACTION
19
B
269 - 356
20
X-RAY DIFFRACTION
20
B
357 - 401
21
X-RAY DIFFRACTION
21
B
402 - 429
22
X-RAY DIFFRACTION
22
B
430 - 469
23
X-RAY DIFFRACTION
23
B
470 - 553
24
X-RAY DIFFRACTION
24
B
554 - 583
+
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