- PDB-3olu: X-ray crystal structure of 1-arachidonoyl glycerol bound to the c... -
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Basic information
Entry
Database: PDB / ID: 3olu
Title
X-ray crystal structure of 1-arachidonoyl glycerol bound to the cyclooxygenase channel of R513H murine COX-2
Components
Prostaglandin G/H synthase 2
Keywords
OXIDOREDUCTASE / Monotopic Membrane Protein / N-glycosylation / Membrane
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 salvage ...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 salvage / Synthesis of Prostaglandins (PG) and Thromboxanes (TX) / positive regulation of fibroblast growth factor production / prostaglandin-endoperoxide synthase / prostaglandin-endoperoxide synthase activity / cyclooxygenase pathway / positive regulation of transforming growth factor beta production / cellular response to lead ion / negative regulation of synaptic transmission, dopaminergic / 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 / response to fatty acid / response to fructose / positive regulation of smooth muscle contraction / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / positive regulation of fever generation / response to vitamin D / prostaglandin secretion / cellular response to fluid shear stress / response to selenium ion / response to nematode / nuclear outer membrane / response to angiotensin / nuclear inner membrane / response to manganese ion / prostaglandin biosynthetic process / negative regulation of smooth muscle contraction / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to ATP / maintenance of blood-brain barrier / bone mineralization / negative regulation of calcium ion transport / negative regulation of cell cycle / decidualization / response to tumor necrosis factor / positive regulation of vascular endothelial growth factor production / 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 / positive regulation of smooth muscle cell proliferation / peroxidase activity / caveola / regulation of blood pressure / memory / positive regulation of protein import into nucleus / cellular response to mechanical stimulus / positive regulation of nitric oxide biosynthetic process / response to estradiol / regulation of cell population proliferation / cellular response to heat / cellular response to lipopolysaccharide / angiogenesis / cellular response to hypoxia / response to oxidative stress / neuron projection / positive regulation of apoptotic process / response to xenobiotic stimulus / negative regulation of cell population proliferation / heme binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / protein homodimerization activity / protein-containing complex / metal ion binding / cytosol / cytoplasm Similarity search - Function
Resolution: 2.35→19.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.588 / SU ML: 0.139 / Cross valid method: THROUGHOUT / σ(F): -6 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2136
3024
5.1 %
RANDOM
Rwork
0.16157
-
-
-
obs
0.16417
56810
99.54 %
-
all
-
59835
-
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parameters
Biso mean: 22.128 Å2
Baniso -1
Baniso -2
Baniso -3
1-
0.59 Å2
0 Å2
0 Å2
2-
-
0.31 Å2
0 Å2
3-
-
-
-0.9 Å2
Refine analyze
Luzzati sigma a obs: 0.293 Å
Refinement step
Cycle: LAST / Resolution: 2.35→19.99 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
8864
0
378
666
9908
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.013
0.022
9577
X-RAY DIFFRACTION
r_angle_refined_deg
1.686
2.005
13010
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.593
5
1116
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
36.572
23.973
443
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
15.022
15
1500
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
14.231
15
44
X-RAY DIFFRACTION
r_chiral_restr
0.097
0.2
1384
X-RAY DIFFRACTION
r_gen_planes_refined
0.006
0.021
7330
X-RAY DIFFRACTION
r_mcbond_it
0.484
1.5
5534
X-RAY DIFFRACTION
r_mcangle_it
0.947
2
8995
X-RAY DIFFRACTION
r_scbond_it
1.922
3
4043
X-RAY DIFFRACTION
r_scangle_it
3.154
4.5
4004
LS refinement shell
Resolution: 2.35→2.41 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.249
213
-
Rwork
0.205
4092
-
obs
-
43041
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
0.7509
1.2304
0.2958
4.7279
0.6976
1.9305
-0.0338
-0.2056
0.0818
0.0117
0.0574
0.3388
-0.1328
-0.2671
-0.0236
0.0862
0.0357
0.0424
0.2777
0.0463
0.1911
1.3614
37.6811
60.0257
2
8.5129
-1.5016
4.3088
8.8648
-1.394
4.0646
0.4999
-0.6573
-1.5543
0.2194
0.3481
0.2391
0.819
-0.6551
-0.848
0.3094
-0.1152
0.0446
0.4607
0.1921
0.5978
-3.1392
18.5827
64.2743
3
4.4499
-0.7632
-2.4837
7.0282
0.0533
9.6039
-0.3104
0.0661
-0.2207
0.001
-0.0914
0.6362
0.3721
-0.4329
0.4018
0.1395
-0.0761
0.0174
0.2519
-0.0001
0.3979
13.5023
3.038
66.2726
4
2.5296
-0.6903
1.0571
4.0309
-1.0124
4.4712
-0.0856
-0.0853
-0.1437
-0.0001
0.0546
0.1835
0.1472
-0.1654
0.031
0.0199
0.0087
0.0051
0.0257
0.0044
0.0421
18.3721
33.7485
53.8737
5
1.5428
-0.9024
-0.0665
1.1306
-0.023
1.2993
-0.0566
-0.2152
0.1574
0.1477
0.0875
-0.0865
-0.1715
0.005
-0.0309
0.0659
0.0001
-0.0075
0.0447
-0.0223
0.0625
26.4715
29.8675
71.0404
6
3.2463
0.1403
1.0979
0.735
-0.27
5.1889
0.0007
0.0147
0.2473
-0.0579
-0.006
-0.1701
-0.0093
0.3084
0.0053
0.0091
-0.0008
0.0336
0.0354
-0.0002
0.1469
50.6
18.934
55.6582
7
5.9029
1.0328
-0.9476
1.9913
-2.7585
4.8805
-0.0349
-0.4222
0.7273
0.0828
-0.1144
-0.2686
-0.2369
0.3877
0.1493
0.0951
0.0061
0.0103
0.1726
-0.0875
0.2843
49.4741
25.8712
65.9961
8
1.0726
-0.7634
0.1344
1.2402
-0.2964
3.7371
0.0523
-0.0332
-0.2003
-0.2426
-0.1077
-0.0189
0.2505
0.2746
0.0554
0.0879
0.0458
0.0163
0.0404
0.0403
0.1041
42.382
9.3251
52.2909
9
0.8467
-0.5718
0.1558
1.1479
-0.4708
2.2561
-0.0346
-0.1533
-0.118
0.0595
0.0732
0.1644
0.216
-0.1295
-0.0386
0.0403
0.0008
0.038
0.0661
0.0406
0.1018
25.1736
15.0791
65.3407
10
5.5646
2.0761
0.2477
5.606
2.3191
3.1686
-0.0246
-0.4605
0.0587
0.4013
0.066
-0.1657
-0.036
0.4118
-0.0414
0.1255
0.0442
-0.0259
0.2286
0.0036
0.0964
47.3081
16.2265
78.4138
11
0.9894
-0.6586
-0.3815
0.9583
0.345
1.0838
-0.0668
-0.2483
-0.0645
0.1173
0.0956
0.1097
-0.0113
-0.1357
-0.0288
0.0802
0.0189
0.028
0.1285
0.0362
0.0705
19.5427
24.8996
72.7338
12
2.1016
-1.5448
-0.854
2.3949
0.144
4.1812
-0.0147
-0.1321
-0.2621
0.0511
0.1118
0.1568
0.5691
-0.1922
-0.0971
0.1518
-0.0434
0.0013
0.0286
0.0424
0.1407
37.9024
3.322
64.0081
13
4.535
0.5646
-1.4207
0.8695
-0.5141
2.5786
0.1678
0.054
-0.2489
-0.2633
-0.1716
0.021
0.5233
0.1958
0.0038
0.4075
0.0604
-0.0447
0.1384
-0.0372
0.1827
33.7671
1.6954
33.1921
14
10.6495
-4.6137
2.303
5.3282
-3.5627
2.6176
0.2427
-0.1198
-0.4975
-0.3853
0.4513
1.1576
0.317
-0.5582
-0.694
0.6101
-0.1258
-0.1173
0.3955
-0.0877
0.5815
15.1809
-0.4239
28.2809
15
5.595
-1.8336
-1.5144
5.2728
1.622
9.1195
-0.1152
0.3482
-0.6173
-0.2314
-0.2444
0.455
0.3708
-0.3834
0.3596
0.3041
-0.1373
-0.0402
0.2559
-0.0949
0.4039
1.1326
18.5317
26.2892
16
3.202
-1.9742
0.6198
2.9709
-0.2735
4.9912
0.1286
0.0755
-0.1094
-0.1765
-0.1737
0.0703
0.3126
-0.1522
0.0451
0.0785
0.0217
-0.0005
0.0253
-0.0032
0.0221
31.8407
19.2922
38.9279
17
1.0999
-0.9542
-0.0769
1.3317
0.0832
1.7714
0.1159
0.1712
0.0567
-0.1999
-0.0758
-0.1256
0.1047
0.2116
-0.0401
0.0899
0.0274
0.0128
0.104
0.0244
0.0793
29.994
27.5285
21.843
18
2.3375
-0.274
1.0351
3.7454
-0.5012
3.5589
-0.0361
0.1996
0.3299
0.2852
-0.0596
-0.2143
-0.3951
0.2799
0.0958
0.0674
-0.0204
0.0074
0.0376
0.0482
0.1146
21.5601
51.4507
38.5446
19
5.0448
1.7365
1.1096
3.2059
-0.4222
1.5565
-0.1044
0.2237
0.3457
-0.453
0.0677
-0.4496
-0.3626
0.549
0.0367
0.2884
-0.2124
0.1635
0.2745
-0.0427
0.282
26.2076
50.0868
28.8326
20
0.9869
-0.4252
0.0566
1.7295
0.3998
1.9375
0.0515
0.1229
-0.0567
-0.0938
-0.0421
0.2341
0.0936
-0.2025
-0.0094
0.0134
-0.0042
-0.0107
0.0508
0.0241
0.0805
12.141
34.0334
36.3893
21
1.4054
0.2779
-1.0794
6.7062
0.6193
2.685
0.208
0.4234
0.3809
-0.5078
-0.0699
-0.2502
-0.2758
0.068
-0.1381
0.1756
0.0712
0.0449
0.2979
0.1353
0.1648
19.5702
48.4233
14.6656
22
2.3548
-0.8588
1.1587
1.4357
-1.276
1.2734
0.0987
0.1876
0.0762
-0.1773
-0.1354
-0.0391
0.1451
0.2109
0.0367
0.2057
0.1109
0.0192
0.2171
-0.0022
0.0505
29.7593
29.803
13.6802
23
1.8198
-0.6704
0.2042
2.2117
-0.0586
3.057
0.1255
0.2739
-0.2188
-0.3241
-0.126
0.1387
0.3377
-0.0552
0.0005
0.253
0.049
-0.0403
0.1277
-0.042
0.0916
25.3925
16.5373
16.885
24
1.23
0.0023
0.0947
1.6681
-1.1794
3.526
0.0753
0.1345
-0.048
-0.0589
0.0796
0.2236
0.0874
-0.3002
-0.1548
0.0106
0.0025
-0.0004
0.055
0.0294
0.1035
6.6738
38.1478
35.8958
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 - 87
3
X-RAY DIFFRACTION
3
A
88 - 122
4
X-RAY DIFFRACTION
4
A
123 - 148
5
X-RAY DIFFRACTION
5
A
149 - 233
6
X-RAY DIFFRACTION
6
A
234 - 268
7
X-RAY DIFFRACTION
7
A
269 - 301
8
X-RAY DIFFRACTION
8
A
302 - 344
9
X-RAY DIFFRACTION
9
A
345 - 399
10
X-RAY DIFFRACTION
10
A
400 - 429
11
X-RAY DIFFRACTION
11
A
430 - 553
12
X-RAY DIFFRACTION
12
A
554 - 583
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 - 151
17
X-RAY DIFFRACTION
17
B
152 - 230
18
X-RAY DIFFRACTION
18
B
231 - 268
19
X-RAY DIFFRACTION
19
B
269 - 308
20
X-RAY DIFFRACTION
20
B
309 - 389
21
X-RAY DIFFRACTION
21
B
390 - 430
22
X-RAY DIFFRACTION
22
B
431 - 457
23
X-RAY DIFFRACTION
23
B
458 - 534
24
X-RAY DIFFRACTION
24
B
535 - 583
+
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