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- PDB-8j6n: Crystal structure of Cystathionine gamma-lyase in complex with co... -

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Basic information

Entry
Database: PDB / ID: 8j6n
TitleCrystal structure of Cystathionine gamma-lyase in complex with compound 1
ComponentsCystathionine gamma-lyase
KeywordsLYASE
Function / homology
Function and homology information


cystathionine gamma-lyase / L-cystine L-cysteine-lyase (deaminating) / cystathionine gamma-lyase activity / cysteine biosynthetic process / L-cysteine desulfhydrase activity / transsulfuration / pyridoxal phosphate binding
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
: / Cystathionine gamma-lyase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHibi, R. / Toma-Fukai, S. / Shimizu, T. / Hanaoka, K.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Sci Rep / Year: 2023
Title: Discovery of a cystathionine gamma-lyase (CSE) selective inhibitor targeting active-site pyridoxal 5'-phosphate (PLP) via Schiff base formation.
Authors: Echizen, H. / Hanaoka, K. / Shimamoto, K. / Hibi, R. / Toma-Fukai, S. / Ohno, H. / Sasaki, E. / Komatsu, T. / Ueno, T. / Tsuchiya, Y. / Watanabe, Y. / Otsuka, T. / Saito, H. / Nagatoishi, S. ...Authors: Echizen, H. / Hanaoka, K. / Shimamoto, K. / Hibi, R. / Toma-Fukai, S. / Ohno, H. / Sasaki, E. / Komatsu, T. / Ueno, T. / Tsuchiya, Y. / Watanabe, Y. / Otsuka, T. / Saito, H. / Nagatoishi, S. / Tsumoto, K. / Kojima, H. / Okabe, T. / Shimizu, T. / Urano, Y.
History
DepositionApr 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
E: Cystathionine gamma-lyase
H: Cystathionine gamma-lyase
J: Cystathionine gamma-lyase
K: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
G: Cystathionine gamma-lyase
I: Cystathionine gamma-lyase
L: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)520,64739
Polymers515,42912
Non-polymers5,21827
Water53,6672979
1
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,50712
Polymers171,8104
Non-polymers1,6978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20690 Å2
ΔGint-126 kcal/mol
Surface area45030 Å2
MethodPISA
2
E: Cystathionine gamma-lyase
H: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
G: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,41511
Polymers171,8104
Non-polymers1,6057
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20420 Å2
ΔGint-123 kcal/mol
Surface area45030 Å2
MethodPISA
3
J: Cystathionine gamma-lyase
K: Cystathionine gamma-lyase
I: Cystathionine gamma-lyase
L: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,72516
Polymers171,8104
Non-polymers1,91512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21520 Å2
ΔGint-104 kcal/mol
Surface area44940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.214, 184.121, 175.944
Angle α, β, γ (deg.)90.00, 99.46, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25H
16A
26J
17A
27K
18A
28F
19A
29G
110A
210I
111A
211L
112B
212C
113B
213D
114B
214E
115B
215H
116B
216J
117B
217K
118B
218F
119B
219G
120B
220I
121B
221L
122C
222D
123C
223E
124C
224H
125C
225J
126C
226K
127C
227F
128C
228G
129C
229I
130C
230L
131D
231E
132D
232H
133D
233J
134D
234K
135D
235F
136D
236G
137D
237I
138D
238L
139E
239H
140E
240J
141E
241K
142E
242F
143E
243G
144E
244I
145E
245L
146H
246J
147H
247K
148H
248F
149H
249G
150H
250I
151H
251L
152J
252K
153J
253F
154J
254G
155J
255I
156J
256L
157K
257F
158K
258G
159K
259I
160K
260L
161F
261G
162F
262I
163F
263L
164G
264I
165G
265L
166I
266L

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA10 - 3993 - 392
21PROPROBB10 - 3993 - 392
12PROPROAA10 - 3993 - 392
22PROPROCC10 - 3993 - 392
13PROPROAA10 - 3993 - 392
23PROPRODD10 - 3993 - 392
14PROPROAA10 - 3993 - 392
24PROPROEE10 - 3993 - 392
15PROPROAA10 - 3993 - 392
25PROPROHF10 - 3993 - 392
16PROPROAA10 - 3993 - 392
26PROPROJG10 - 3993 - 392
17PROPROAA10 - 3993 - 392
27PROPROKH10 - 3993 - 392
18PROPROAA10 - 3993 - 392
28PROPROFI10 - 3993 - 392
19ALAALAAA10 - 3973 - 390
29ALAALAGJ10 - 3973 - 390
110PROPROAA10 - 3993 - 392
210PROPROIK10 - 3993 - 392
111PROPROAA10 - 3993 - 392
211PROPROLL10 - 3993 - 392
112PROPROBB10 - 3993 - 392
212PROPROCC10 - 3993 - 392
113PROPROBB10 - 3993 - 392
213PROPRODD10 - 3993 - 392
114PROPROBB10 - 3993 - 392
214PROPROEE10 - 3993 - 392
115PROPROBB10 - 3993 - 392
215PROPROHF10 - 3993 - 392
116PROPROBB10 - 3993 - 392
216PROPROJG10 - 3993 - 392
117PROPROBB10 - 3993 - 392
217PROPROKH10 - 3993 - 392
118PROPROBB10 - 3993 - 392
218PROPROFI10 - 3993 - 392
119ALAALABB10 - 3973 - 390
219ALAALAGJ10 - 3973 - 390
120PROPROBB10 - 3993 - 392
220PROPROIK10 - 3993 - 392
121PROPROBB10 - 3993 - 392
221PROPROLL10 - 3993 - 392
122PROPROCC10 - 3993 - 392
222PROPRODD10 - 3993 - 392
123PROPROCC10 - 3993 - 392
223PROPROEE10 - 3993 - 392
124PROPROCC10 - 3993 - 392
224PROPROHF10 - 3993 - 392
125PROPROCC10 - 3993 - 392
225PROPROJG10 - 3993 - 392
126PROPROCC10 - 3993 - 392
226PROPROKH10 - 3993 - 392
127PROPROCC10 - 3993 - 392
227PROPROFI10 - 3993 - 392
128ALAALACC10 - 3973 - 390
228ALAALAGJ10 - 3973 - 390
129PROPROCC10 - 3993 - 392
229PROPROIK10 - 3993 - 392
130PROPROCC10 - 3993 - 392
230PROPROLL10 - 3993 - 392
131PROPRODD10 - 3993 - 392
231PROPROEE10 - 3993 - 392
132PROPRODD10 - 3993 - 392
232PROPROHF10 - 3993 - 392
133PROPRODD10 - 3993 - 392
233PROPROJG10 - 3993 - 392
134PROPRODD10 - 3993 - 392
234PROPROKH10 - 3993 - 392
135PROPRODD10 - 3993 - 392
235PROPROFI10 - 3993 - 392
136ALAALADD10 - 3973 - 390
236ALAALAGJ10 - 3973 - 390
137PROPRODD10 - 3993 - 392
237PROPROIK10 - 3993 - 392
138PROPRODD10 - 3993 - 392
238PROPROLL10 - 3993 - 392
139PROPROEE10 - 3993 - 392
239PROPROHF10 - 3993 - 392
140PROPROEE10 - 3993 - 392
240PROPROJG10 - 3993 - 392
141PROPROEE10 - 3993 - 392
241PROPROKH10 - 3993 - 392
142PROPROEE10 - 3993 - 392
242PROPROFI10 - 3993 - 392
143ALAALAEE10 - 3973 - 390
243ALAALAGJ10 - 3973 - 390
144PROPROEE10 - 3993 - 392
244PROPROIK10 - 3993 - 392
145PROPROEE10 - 3993 - 392
245PROPROLL10 - 3993 - 392
146PROPROHF10 - 3993 - 392
246PROPROJG10 - 3993 - 392
147PROPROHF10 - 3993 - 392
247PROPROKH10 - 3993 - 392
148PROPROHF10 - 3993 - 392
248PROPROFI10 - 3993 - 392
149ALAALAHF10 - 3973 - 390
249ALAALAGJ10 - 3973 - 390
150PROPROHF10 - 3993 - 392
250PROPROIK10 - 3993 - 392
151PROPROHF10 - 3993 - 392
251PROPROLL10 - 3993 - 392
152PROPROJG10 - 3993 - 392
252PROPROKH10 - 3993 - 392
153PROPROJG10 - 3993 - 392
253PROPROFI10 - 3993 - 392
154ALAALAJG10 - 3973 - 390
254ALAALAGJ10 - 3973 - 390
155PROPROJG10 - 3993 - 392
255PROPROIK10 - 3993 - 392
156PROPROJG10 - 3993 - 392
256PROPROLL10 - 3993 - 392
157PROPROKH10 - 3993 - 392
257PROPROFI10 - 3993 - 392
158ALAALAKH10 - 3973 - 390
258ALAALAGJ10 - 3973 - 390
159PROPROKH10 - 3993 - 392
259PROPROIK10 - 3993 - 392
160PROPROKH10 - 3993 - 392
260PROPROLL10 - 3993 - 392
161ALAALAFI10 - 3973 - 390
261ALAALAGJ10 - 3973 - 390
162PROPROFI10 - 3993 - 392
262PROPROIK10 - 3993 - 392
163PROPROFI10 - 3993 - 392
263PROPROLL10 - 3993 - 392
164ALAALAGJ10 - 3973 - 390
264ALAALAIK10 - 3973 - 390
165ALAALAGJ10 - 3973 - 390
265ALAALALL10 - 3973 - 390
166PROPROIK10 - 3993 - 392
266PROPROLL10 - 3993 - 392

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66

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Components

#1: Protein
Cystathionine gamma-lyase / / Cysteine-protein sulfhydrase / Gamma-cystathionase


Mass: 42952.457 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Cth, CSE / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EQS4, cystathionine gamma-lyase
#2: Chemical
ChemComp-TVJ / [6-methyl-4-[(~{E})-(oxamoylhydrazinylidene)methyl]-5-oxidanyl-pyridin-3-yl]methyl dihydrogen phosphate


Mass: 332.207 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C10H13N4O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2979 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 54.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.18 M tri-Ammonium citrate, 20% Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.9→48.98 Å / Num. obs: 430998 / % possible obs: 99.4 % / Redundancy: 3.8 % / CC1/2: 0.994 / Net I/σ(I): 7.8
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 20919 / CC1/2: 0.729

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→48.98 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.143 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 21313 5 %RANDOM
Rwork0.17247 ---
obs0.17362 409120 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.575 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35980 0 344 2979 39303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01337627
X-RAY DIFFRACTIONr_bond_other_d0.0010.01536260
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.6451129
X-RAY DIFFRACTIONr_angle_other_deg1.4011.57583774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.21754875
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.71421.9571753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.814156516
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.63315208
X-RAY DIFFRACTIONr_chiral_restr0.0830.25014
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0242474
X-RAY DIFFRACTIONr_gen_planes_other0.0010.028278
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.092.10918918
X-RAY DIFFRACTIONr_mcbond_other2.0882.10918917
X-RAY DIFFRACTIONr_mcangle_it2.9893.15323681
X-RAY DIFFRACTIONr_mcangle_other2.993.15323682
X-RAY DIFFRACTIONr_scbond_it3.3942.51518709
X-RAY DIFFRACTIONr_scbond_other3.3942.51518710
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3083.59827347
X-RAY DIFFRACTIONr_long_range_B_refined6.62126.00841854
X-RAY DIFFRACTIONr_long_range_B_other6.54725.71641278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A128100.05
12B128100.05
21A128110.05
22C128110.05
31A128210.05
32D128210.05
41A127930.05
42E127930.05
51A127540.05
52H127540.05
61A127940.05
62J127940.05
71A127510.05
72K127510.05
81A128160.05
82F128160.05
91A126770.05
92G126770.05
101A127740.05
102I127740.05
111A127370.06
112L127370.06
121B128650.05
122C128650.05
131B128230.06
132D128230.06
141B128200.06
142E128200.06
151B128010.06
152H128010.06
161B128290.06
162J128290.06
171B128110.05
172K128110.05
181B128320.06
182F128320.06
191B127140.05
192G127140.05
201B128210.06
202I128210.06
211B127740.06
212L127740.06
221C129190.05
222D129190.05
231C128750.05
232E128750.05
241C128570.05
242H128570.05
251C128670.05
252J128670.05
261C128200.05
262K128200.05
271C128700.05
272F128700.05
281C127600.05
282G127600.05
291C128540.05
292I128540.05
301C128620.05
302L128620.05
311D128210.05
312E128210.05
321D128060.05
322H128060.05
331D128330.05
332J128330.05
341D127940.05
342K127940.05
351D128480.05
352F128480.05
361D127170.05
362G127170.05
371D128020.06
372I128020.06
381D128110.05
382L128110.05
391E127660.05
392H127660.05
401E128110.05
402J128110.05
411E127300.06
412K127300.06
421E128060.05
422F128060.05
431E126600.05
432G126600.05
441E127960.05
442I127960.05
451E127160.05
452L127160.05
461H127850.06
462J127850.06
471H128270.04
472K128270.04
481H128110.05
482F128110.05
491H127570.04
492G127570.04
501H127940.05
502I127940.05
511H128330.04
512L128330.04
521J128200.05
522K128200.05
531J128960.04
532F128960.04
541J127420.05
542G127420.05
551J128540.05
552I128540.05
561J127880.06
562L127880.06
571K128060.05
572F128060.05
581K127610.04
582G127610.04
591K127650.06
592I127650.06
601K127990.05
602L127990.05
611F127300.05
612G127300.05
621F128330.06
622I128330.06
631F127960.06
632L127960.06
641G127100.05
642I127100.05
651G127570.04
652L127570.04
661I127680.05
662L127680.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 1603 -
Rwork0.263 30173 -
obs--99.8 %

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