- PDB-3qh0: X-ray crystal structure of palmitic acid bound to the cyclooxygen... -
+
Open data
ID or keywords:
Loading...
-
Basic information
Entry
Database: PDB / ID: 3qh0
Title
X-ray crystal structure of palmitic acid bound to the cyclooxygenase channel of cyclooxygenase-2
Components
Prostaglandin G/H synthase 2
Keywords
OXIDOREDUCTASE / Biological Dimer / 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 / hair cycle / cellular response to homocysteine / Nicotinamide salvaging ...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 / hair cycle / cellular response to homocysteine / Nicotinamide salvaging / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / negative regulation of synaptic transmission, dopaminergic / cellular response to lead ion / response to nematode / positive regulation of transforming growth factor beta production / negative regulation of intrinsic apoptotic signaling pathway in response to osmotic stress / positive regulation of prostaglandin biosynthetic process / regulation of neuroinflammatory response / positive regulation of synaptic plasticity / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / cyclooxygenase pathway / response to fatty acid / response to fructose / positive regulation of fever generation / prostaglandin secretion / response to vitamin D / cellular response to fluid shear stress / nuclear outer membrane / response to angiotensin / response to manganese ion / prostaglandin biosynthetic process / nuclear inner membrane / negative regulation of smooth muscle contraction / cellular response to ATP / positive regulation of cell migration involved in sprouting angiogenesis / maintenance of blood-brain barrier / bone mineralization / negative regulation of calcium ion transport / decidualization / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / response to tumor necrosis factor / brown fat cell differentiation / response to glucocorticoid / keratinocyte differentiation / positive regulation of vasoconstriction / positive regulation of brown fat cell differentiation / embryo implantation / positive regulation of synaptic transmission, glutamatergic / learning / response to cytokine / caveola / positive regulation of smooth muscle cell proliferation / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / memory / regulation of blood pressure / positive regulation of protein import into nucleus / peroxidase activity / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / positive regulation of peptidyl-serine phosphorylation / response to estradiol / cellular response to heat / regulation of cell population proliferation / cellular response to hypoxia / angiogenesis / response to oxidative stress / response to lipopolysaccharide / response to xenobiotic stimulus / neuron projection / positive regulation of apoptotic process / negative regulation of cell population proliferation / heme binding / positive regulation of cell population proliferation / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / metal ion binding / cytoplasm Similarity search - Function
Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.901 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.19894
4122
5 %
RANDOM
Rwork
0.15947
-
-
-
all
0.211
82053
-
-
obs
0.16145
77928
97.9 %
-
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: 28.188 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0 Å2
0 Å2
0 Å2
2-
-
-0.05 Å2
0 Å2
3-
-
-
0.05 Å2
Refine analyze
Luzzati sigma a obs: 0.257 Å
Refinement step
Cycle: LAST / Resolution: 2.1→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8833
0
377
753
9963
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.011
0.022
9570
X-RAY DIFFRACTION
r_angle_refined_deg
1.329
2.001
13009
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.692
5
1129
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
37.361
23.924
446
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.632
15
1482
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.88
15
46
X-RAY DIFFRACTION
r_chiral_restr
0.093
0.2
1380
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
7344
X-RAY DIFFRACTION
r_mcbond_it
0.502
1.5
5565
X-RAY DIFFRACTION
r_mcangle_it
0.97
2
9044
X-RAY DIFFRACTION
r_scbond_it
1.841
3
4005
X-RAY DIFFRACTION
r_scangle_it
3.063
4.5
3952
LS refinement shell
Resolution: 2.1→2.154 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.276
310
-
Rwork
0.211
5576
-
obs
-
-
96.52 %
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
1.0567
-0.0687
0.1704
3.8869
1.0562
1.985
-0.0529
-0.2515
0.0305
0.0506
0.1627
0.0524
-0.1368
-0.5552
-0.1097
0.0594
0.0664
0.0495
0.2753
0.0758
0.1489
1.3394
37.1273
59.892
2
4.9645
-3.2354
4.1029
9.9081
-5.1141
4.1743
0.2881
-0.3324
-0.8992
-0.4332
0.5422
0.7747
0.352
-0.4681
-0.8303
0.2147
-0.1428
0.0409
0.5097
0.1654
0.4432
-3.5201
18.1978
63.7919
3
1.8541
-0.2957
-1.2977
4.1887
-0.7335
6.7349
-0.109
-0.0229
-0.4238
0.0914
0.0543
0.2639
0.9159
-0.7527
0.0547
0.1581
-0.1614
0.0069
0.2294
0.0579
0.3367
13.2572
2.374
66.6624
4
0.5823
-0.3063
0.1925
0.6588
-0.4991
1.6769
-0.1028
-0.1532
0.0351
0.1144
0.1555
0.032
-0.1028
-0.1831
-0.0526
0.0711
0.0664
0.006
0.1059
0.0074
0.066
18.3088
35.4625
66.3008
5
0.8995
-0.8327
0.1379
1.0728
-0.2955
1.6292
-0.0628
-0.1261
0.0705
0.0834
0.0895
-0.1018
-0.0349
-0.0293
-0.0266
0.0285
0.0067
-0.011
0.0418
-0.0094
0.0629
33.2293
22.8
66.6822
6
2.1833
-0.0524
0.862
1.7125
-0.3659
2.2638
0.1239
0.0527
0.0733
-0.0476
-0.0058
-0.1649
-0.02
0.26
-0.118
0.0203
0.0046
0.0296
0.0472
-0.008
0.1319
51.5671
19.0139
55.7902
7
5.3535
0.5336
-1.0888
3.4482
-1.2187
4.8179
-0.0794
-0.3901
0.5118
0.1102
0.0015
-0.292
-0.3354
0.2622
0.0779
0.0492
-0.0116
0.0262
0.0532
-0.0636
0.2295
50.6128
26.8737
65.6095
8
1.3031
-0.3199
-0.0334
0.7833
-0.2515
1.1876
0.0521
-0.0525
-0.1195
-0.0386
0.003
0.0837
0.1689
-0.0251
-0.055
0.0659
-0.0039
-0.0282
0.004
0.0116
0.0926
33.8904
9.4197
56.2276
9
1.8318
-0.9555
1.5889
1.4795
-1.3725
4.0377
-0.1121
-0.3429
0.0369
0.2293
0.1652
-0.0143
-0.0742
-0.0985
-0.0531
0.076
0.0379
0.012
0.0863
-0.0108
0.0234
31.9689
22.1374
73.5913
10
3.1558
-0.9282
-0.7587
1.0357
0.2991
1.6793
-0.0588
-0.3008
0.1569
0.1816
0.1935
-0.1337
-0.0364
0.179
-0.1347
0.0967
0.0486
-0.0354
0.1573
-0.0283
0.0318
41.9121
18.0007
79.9808
11
0.6755
-0.5657
-0.1355
0.8506
0.3026
1.0947
-0.0796
-0.2153
-0.0706
0.1379
0.1209
0.11
-0.0283
-0.1927
-0.0413
0.0567
0.0356
0.0278
0.1362
0.0442
0.0629
18.2532
24.7263
71.4308
12
1.3668
-0.5151
0.2208
2.9647
0.8477
3.7331
-0.0961
-0.148
-0.4013
0.0551
0.0502
0.2406
0.3826
-0.2077
0.0458
0.1187
-0.0034
-0.0065
0.035
0.0381
0.1546
38.0055
2.9948
64.4858
13
2.9754
-0.1115
-1.125
0.3923
-0.0297
2.363
0.1084
0.0284
-0.0427
-0.2478
-0.0395
0.0117
0.5275
0.0547
-0.069
0.3103
0.063
-0.0618
0.0534
-0.0456
0.1601
34.4097
1.9099
33.1464
14
15.9484
2.0424
1.5208
2.4515
-0.3607
2.5035
-0.2384
-0.052
-0.4182
-0.0816
0.1468
0.3555
0.3138
-0.3471
0.0916
0.3346
-0.0522
-0.07
0.1334
-0.0527
0.2644
18.7895
-3.7018
30.1323
15
2.3969
-1.2917
-0.6623
2.1782
2.3904
5.2192
0.0365
0.1937
-0.4712
0.1566
-0.3866
0.4277
0.6574
-0.7484
0.3501
0.2704
-0.1501
-0.0543
0.1863
-0.086
0.3904
2.1954
16.6729
25.0434
16
0.5947
-0.1048
0.2798
0.5184
-0.1524
1.5008
0.1399
0.112
-0.1026
-0.2033
-0.1604
0.0105
0.2096
0.1235
0.0205
0.1308
0.1024
0.0004
0.0822
-0.0036
0.0515
34.3348
19.3274
26.3919
17
0.7912
-0.8136
0.1186
1.0323
-0.1528
1.2503
0.0404
0.0801
0.0558
-0.0845
-0.0641
-0.0629
0.0116
0.1389
0.0237
0.0625
0.0269
0.0048
0.0567
0.0201
0.082
24.2521
34.7795
28.0386
18
1.6692
-0.3781
0.7073
2.6959
-1.0446
2.8517
-0.1123
-0.0142
0.2588
0.1809
0.0748
-0.1658
-0.3157
0.1079
0.0375
0.0665
-0.011
-0.0226
0.0141
0.0008
0.099
21.6925
52.7082
38.8209
19
1.3472
0.8824
0.1328
7.7115
5.2232
9.1587
-0.4989
0.2613
0.2689
-1.147
0.4025
-0.6736
-1.3388
1.1241
0.0965
0.4071
-0.2397
-0.026
0.3325
0.09
0.3694
31.592
54.5075
29.0998
20
0.7768
-0.2174
0.1436
1.2224
0.0876
1.2314
0.0094
0.0169
-0.0581
-0.0475
0.0145
0.113
0.0042
-0.0954
-0.0239
0.0121
0.0128
-0.0166
0.0553
0.0203
0.0708
11.9862
37.6197
36.1886
21
0.6783
-0.7495
0.3859
3.0221
-1.5934
2.1355
0.2083
0.2358
0.0589
-0.3966
-0.2078
-0.0524
0.047
0.3079
-0.0005
0.0985
0.0466
0.0298
0.1597
0.0214
0.0482
24.3669
40.5599
17.9436
22
2.8639
1.8539
0.6332
11.7041
2.2756
4.46
0.069
0.2082
0.0596
-0.1694
0.0581
-0.0235
-0.1169
0.0316
-0.1272
0.1074
0.0439
-0.0014
0.1285
0.0217
0.0908
12.8664
49.7504
16.7382
23
1.169
-0.3295
0.8164
1.434
-0.3672
0.9758
0.2036
0.2538
-0.0309
-0.2803
-0.189
0.0289
0.1901
0.2156
-0.0147
0.1753
0.12
0.0108
0.1387
-0.0121
0.0098
30.557
25.4508
16.8981
24
0.8854
-0.4827
0.0145
0.7145
-0.2688
0.6536
0.1177
0.1463
-0.1451
-0.1968
-0.0787
0.1283
0.2014
-0.0269
-0.039
0.1051
0.0169
-0.0635
0.0607
-0.0121
0.0762
17.033
25.5901
23.7865
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 - 86
3
X-RAY DIFFRACTION
3
A
87 - 120
4
X-RAY DIFFRACTION
4
A
121 - 186
5
X-RAY DIFFRACTION
5
A
187 - 235
6
X-RAY DIFFRACTION
6
A
236 - 268
7
X-RAY DIFFRACTION
7
A
269 - 296
8
X-RAY DIFFRACTION
8
A
297 - 375
9
X-RAY DIFFRACTION
9
A
376 - 400
10
X-RAY DIFFRACTION
10
A
401 - 445
11
X-RAY DIFFRACTION
11
A
446 - 553
12
X-RAY DIFFRACTION
12
A
554 - 584
13
X-RAY DIFFRACTION
13
B
33 - 66
14
X-RAY DIFFRACTION
14
B
67 - 81
15
X-RAY DIFFRACTION
15
B
82 - 120
16
X-RAY DIFFRACTION
16
B
121 - 188
17
X-RAY DIFFRACTION
17
B
189 - 234
18
X-RAY DIFFRACTION
18
B
235 - 268
19
X-RAY DIFFRACTION
19
B
269 - 286
20
X-RAY DIFFRACTION
20
B
287 - 376
21
X-RAY DIFFRACTION
21
B
377 - 416
22
X-RAY DIFFRACTION
22
B
417 - 429
23
X-RAY DIFFRACTION
23
B
430 - 468
24
X-RAY DIFFRACTION
24
B
469 - 583
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi