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- PDB-5tzx: CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 1... -

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Basic information

Entry
Database: PDB / ID: 5tzx
TitleCRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 2A IN COMPLEX WITH 1-[(3-chloro-4-fluorophenyl)carbonyl]-3,3-difluoro-5-{5-methyl-[1,2,4]triazolo[1,5-a]pyrimidin-7-yl}piperidine
ComponentscGMP-dependent 3',5'-cyclic phosphodiesterase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / phosphodiesterase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / heart valve development / positive regulation of vascular permeability / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier ...regulation of cGMP-mediated signaling / cellular response to 2,3,7,8-tetrachlorodibenzodioxine / cellular response to macrophage colony-stimulating factor stimulus / cellular response to cGMP / negative regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / heart valve development / positive regulation of vascular permeability / cellular response to granulocyte macrophage colony-stimulating factor stimulus / negative regulation of vascular permeability / establishment of endothelial barrier / negative regulation of cAMP-mediated signaling / regulation of mitochondrion organization / aorta development / ventricular septum development / cGMP-stimulated cyclic-nucleotide phosphodiesterase activity / 3',5'-cyclic-nucleotide phosphodiesterase / negative regulation of cGMP-mediated signaling / TPR domain binding / cGMP catabolic process / phosphate ion binding / cGMP effects / cGMP-mediated signaling / monocyte differentiation / cGMP binding / 3',5'-cyclic-GMP phosphodiesterase activity / 3',5'-cyclic-AMP phosphodiesterase activity / regulation of cAMP-mediated signaling / cAMP binding / cellular response to cAMP / cellular response to transforming growth factor beta stimulus / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / cAMP-mediated signaling / synaptic membrane / positive regulation of inflammatory response / cellular response to mechanical stimulus / cellular response to xenobiotic stimulus / presynaptic membrane / G alpha (s) signalling events / mitochondrial outer membrane / mitochondrial inner membrane / mitochondrial matrix / positive regulation of gene expression / perinuclear region of cytoplasm / Golgi apparatus / negative regulation of transcription by RNA polymerase II / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / zinc ion binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. ...Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase / GAF domain / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain / 3'5'-cyclic nucleotide phosphodiesterase, conserved site / 3'5'-cyclic nucleotide phosphodiesterase, catalytic domain superfamily / 3'5'-cyclic nucleotide phosphodiesterase / 3'5'-cyclic nucleotide phosphodiesterase domain signature. / 3'5'-cyclic nucleotide phosphodiesterase domain profile. / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7OY / cGMP-dependent 3',5'-cyclic phosphodiesterase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å
AuthorsXu, R. / Aertgeerts, K.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Design and Synthesis of Novel and Selective Phosphodiesterase 2 (PDE2a) Inhibitors for the Treatment of Memory Disorders.
Authors: Gomez, L. / Massari, M.E. / Vickers, T. / Freestone, G. / Vernier, W. / Ly, K. / Xu, R. / McCarrick, M. / Marrone, T. / Metz, M. / Yan, Y.G. / Yoder, Z.W. / Lemus, R. / Broadbent, N.J. / ...Authors: Gomez, L. / Massari, M.E. / Vickers, T. / Freestone, G. / Vernier, W. / Ly, K. / Xu, R. / McCarrick, M. / Marrone, T. / Metz, M. / Yan, Y.G. / Yoder, Z.W. / Lemus, R. / Broadbent, N.J. / Barido, R. / Warren, N. / Schmelzer, K. / Neul, D. / Lee, D. / Andersen, C.B. / Sebring, K. / Aertgeerts, K. / Zhou, X. / Tabatabaei, A. / Peters, M. / Breitenbucher, J.G.
History
DepositionNov 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2017Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,67016
Polymers160,6724
Non-polymers1,99812
Water12,304683
1
A: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6684
Polymers40,1681
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6684
Polymers40,1681
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6684
Polymers40,1681
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: cGMP-dependent 3',5'-cyclic phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6684
Polymers40,1681
Non-polymers5003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.669, 72.703, 90.360
Angle α, β, γ (deg.)109.280, 90.960, 90.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
cGMP-dependent 3',5'-cyclic phosphodiesterase / Cyclic GMP-stimulated phosphodiesterase / cGSPDE


Mass: 40168.051 Da / Num. of mol.: 4 / Fragment: catalytic domain, UNP residues 323-663
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDE2A / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): baculovirus insect cell Hi5
References: UniProt: O00408, 3',5'-cyclic-nucleotide phosphodiesterase
#2: Chemical
ChemComp-7OY / (3-chloro-4-fluorophenyl)[(5S)-3,3-difluoro-5-(5-methyl[1,2,4]triazolo[1,5-a]pyrimidin-7-yl)piperidin-1-yl]methanone


Mass: 409.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C18H15ClF3N5O
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 683 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 17-19% PEG3350, 0.2M MgCl2, 0.1M Tris, pH 8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.9→64.96 Å / Num. obs: 102462 / % possible obs: 97.3 % / Redundancy: 2 % / Biso Wilson estimate: 18.26 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 6.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2 % / Rmerge(I) obs: 0.549 / % possible all: 96.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 56

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Processing

Software
NameVersionClassification
xia2data scaling
PHASERphasing
PHENIX(1.10.1-2155_1692: ???)refinement
PDB_EXTRACT3.2data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→64.958 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 36.21
RfactorNum. reflection% reflection
Rfree0.3065 4969 4.87 %
Rwork0.2475 --
obs0.2503 102034 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.22 Å2 / Biso mean: 22.632 Å2 / Biso min: 2.03 Å2
Refinement stepCycle: final / Resolution: 1.9→64.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11033 0 0 683 11716
Biso mean---22.91 -
Num. residues----1346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711301
X-RAY DIFFRACTIONf_angle_d0.88215268
X-RAY DIFFRACTIONf_chiral_restr0.0451625
X-RAY DIFFRACTIONf_plane_restr0.0061972
X-RAY DIFFRACTIONf_dihedral_angle_d14.236762
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.92160.39041540.3863232338695
1.9216-1.94420.42061790.38123101328095
1.9442-1.96790.43621730.36873218339195
1.9679-1.99280.40761650.34983178334396
1.9928-2.0190.41521650.34113225339096
2.019-2.04670.36571650.33343164332996
2.0467-2.07590.37291430.32933246338996
2.0759-2.10690.36631560.31173218337496
2.1069-2.13990.35381560.31373266342296
2.1399-2.17490.35841610.30093170333197
2.1749-2.21250.32721740.30643264343896
2.2125-2.25270.41731680.3183201336996
2.2527-2.2960.38221510.30943217336896
2.296-2.34290.38781470.29133274342197
2.3429-2.39380.331640.27863229339397
2.3938-2.44950.35011790.26693268344797
2.4495-2.51080.32331720.26323202337497
2.5108-2.57870.35481490.2413241339097
2.5787-2.65450.27681640.24393275343997
2.6545-2.74020.32551990.23683192339197
2.7402-2.83820.26582090.22633194340397
2.8382-2.95180.28851670.23013267343497
2.9518-3.08610.29711640.2263250341497
3.0861-3.24880.21311610.20513249341098
3.2488-3.45240.24541800.19843253343397
3.4524-3.71890.25091630.19573270343398
3.7189-4.09310.2947870.18883326341398
4.0931-4.68530.2451840.17933280346499
4.6853-5.90230.28231510.21653325347699
5.9023-64.99560.26522190.22343270348999
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.55970.39380.45991.04690.05310.6880.0924-0.3787-0.25640.0245-0.058-0.10970.0686-0.0933-0.01160.1984-0.01630.01140.2550.04860.1963-8.743-16.0992.0617
20.7013-0.06230.5081.0159-0.36021.70140.1264-0.0196-0.28680.1907-0.04880.17820.2582-0.1602-0.05390.1349-0.04810.00120.20960.02650.1849-12.8227-12.0026-5.6278
31.52620.13450.43060.719-0.06211.14510.0227-0.0266-0.0469-0.06440.01370.02030.0129-0.0379-0.02340.1213-0.01140.01370.1004-0.00870.097-0.8429-3.6321-9.7201
42.26-1.93960.59761.7388-0.72990.8742-0.003-0.14210.8239-0.1218-0.05260.0014-0.54020.123-0.21410.35320.0143-0.02810.1289-0.07930.333-1.951816.7214-4.8694
52.3297-0.62721.21821.7904-1.04862.288-0.1148-0.48330.3686-0.20960.06410.2085-0.1904-0.36370.01730.20570.0423-0.03730.0328-0.03570.2043-8.16288.8416-4.2719
61.641-0.2930.31550.9053-0.07690.82290.0485-0.20810.15940.1506-0.0663-0.0799-0.24390.25050.01430.2309-0.0182-0.04650.3135-0.02030.170610.4295.78947.5699
71.9252-0.49071.21420.1301-0.25270.7467-0.2175-0.30070.09330.18770.1068-0.1262-0.0137-0.05770.00310.34680.06130.03720.5047-0.08560.25648.88995.54720.7096
80.8627-0.0465-0.22441.2546-0.051.3343-0.02470.0225-0.2192-0.0563-0.0132-0.17680.2250.29740.0340.19790.0280.00040.1209-0.01160.20325.0422-12.7436-37.5614
91.19560.0763-0.12371.05370.16041.2383-0.0150.040.1054-0.04290.01510.0034-0.1647-0.14430.01130.15590.00450.0020.11610.00910.120214.80792.4124-36.9702
102.01880.25880.98960.56520.10140.4237-0.0740.1017-0.0984-0.40870.04070.2751-0.05260.1711-0.07050.38650.01720.08750.48110.0590.12127.5946-0.2758-60.5269
110.872-0.0591-0.24630.9718-0.50852.12640.00540.0556-0.1916-0.1071-0.1094-0.28770.25480.71860.0770.14940.03250.02150.3141-0.01330.253954.0306-42.7554-37.0159
121.8232-0.2834-0.50390.6131-0.18780.8775-0.04950.1372-0.0020.12330.0203-0.0095-0.0762-0.199-0.02610.136-0.00050.00020.1359-0.00950.150533.8081-38.4733-27.2352
131.7695-0.384-0.03240.80960.36511.36090.1287-0.17350.1705-0.1572-0.0109-0.199-0.3170.1292-0.04540.2359-0.02440.05090.1606-0.03720.193449.8207-29.6031-27.6412
141.3492-0.0394-0.22860.87420.24981.93550.31830.240.145-0.1856-0.2070.0338-0.3767-0.70390.00660.26810.0302-0.00290.2981-0.03740.193136.5456-32.5534-44.6259
154.41270.8762.23631.3340.70851.46340.3990.45150.1744-0.2541-0.2798-0.0093-0.28630.16180.06740.42250.0040.090.4940.02660.159245.6793-29.1589-55.1863
161.50850.03360.95810.64190.47461.832-0.0027-0.23850.07430.32930.0753-0.1360.1561-0.14230.00790.3647-0.0408-0.19240.711-0.00410.123921.9996-41.2889-65.5215
170.8214-0.2539-0.0280.5276-0.41620.7258-0.1198-0.4438-0.3170.19040.09640.27270.2865-0.08410.03470.2624-0.04390.06960.55950.10410.261715.3748-41.056111.2055
180.80410.20260.18610.8299-0.0211.00060.1197-0.3167-0.2562-0.0349-0.06510.24420.162-0.36890.0030.1391-0.03590.01410.24720.03220.224718.155-39.5285-1.4284
191.65350.1163-0.15230.52950.18320.95110.06210.1889-0.2077-0.0470.01920.04480.02740.0302-0.06850.1399-0.0233-0.01390.13250.00690.175629.9124-37.2373-12.0818
201.2323-0.69340.25110.7596-0.11830.3239-0.00620.00560.0283-0.04210.00420.0578-0.072-0.07980.01640.09570.02310.0140.22630.00990.145524.3994-16.8415-4.99
211.4311-0.61230.92261.5161-0.56591.39660.0489-0.110.06450.1204-0.00730.0418-0.14750.1466-0.00450.1110.01630.01280.25540.0210.108523.0934-25.7836-0.6472
221.4782-0.9290.14790.82920.03830.6030.1092-0.29850.041-0.01490.0216-0.06020.01390.0468-0.06820.16620.0129-0.02220.33750.01070.151639.0125-28.88228.8797
231.4891-0.4181.29410.4231-0.32351.11280.0083-0.216-0.06760.0890.05750.00320.0701-0.1713-0.01950.26360.0340.00890.4381-0.01640.173237.7255-27.99221.904
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 576 through 611 )A576 - 611
2X-RAY DIFFRACTION2chain 'A' and (resid 612 through 635 )A612 - 635
3X-RAY DIFFRACTION3chain 'A' and (resid 636 through 768 )A636 - 768
4X-RAY DIFFRACTION4chain 'A' and (resid 769 through 786 )A769 - 786
5X-RAY DIFFRACTION5chain 'A' and (resid 787 through 815 )A787 - 815
6X-RAY DIFFRACTION6chain 'A' and (resid 816 through 878 )A816 - 878
7X-RAY DIFFRACTION7chain 'A' and (resid 879 through 917 )A879 - 917
8X-RAY DIFFRACTION8chain 'B' and (resid 579 through 695 )B579 - 695
9X-RAY DIFFRACTION9chain 'B' and (resid 696 through 878 )B696 - 878
10X-RAY DIFFRACTION10chain 'B' and (resid 879 through 915 )B879 - 915
11X-RAY DIFFRACTION11chain 'C' and (resid 590 through 695 )C590 - 695
12X-RAY DIFFRACTION12chain 'C' and (resid 696 through 738 )C696 - 738
13X-RAY DIFFRACTION13chain 'C' and (resid 739 through 792 )C739 - 792
14X-RAY DIFFRACTION14chain 'C' and (resid 793 through 878 )C793 - 878
15X-RAY DIFFRACTION15chain 'C' and (resid 879 through 897 )C879 - 897
16X-RAY DIFFRACTION16chain 'C' and (resid 898 through 916 )C898 - 916
17X-RAY DIFFRACTION17chain 'D' and (resid 590 through 611 )D590 - 611
18X-RAY DIFFRACTION18chain 'D' and (resid 612 through 695 )D612 - 695
19X-RAY DIFFRACTION19chain 'D' and (resid 696 through 768 )D696 - 768
20X-RAY DIFFRACTION20chain 'D' and (resid 769 through 792 )D769 - 792
21X-RAY DIFFRACTION21chain 'D' and (resid 793 through 815 )D793 - 815
22X-RAY DIFFRACTION22chain 'D' and (resid 816 through 878 )D816 - 878
23X-RAY DIFFRACTION23chain 'D' and (resid 879 through 917 )D879 - 917

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  • 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

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