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- PDB-2ixf: Crystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q... -

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Basic information

Entry
Database: PDB / ID: 2ixf
TitleCrystal structure of the ATPase domain of TAP1 with ATP (D645Q, Q678H mutant)
ComponentsANTIGEN PEPTIDE TRANSPORTER 1
KeywordsHYDROLASE / MEMBRANE / TRANSPORT / ABC PROTEIN TRANSPORT / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


tapasin binding / TAP complex / ABC-type peptide antigen transporter activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / ABC-type peptide transporter activity / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / peptide antigen transport / MHC class Ib protein binding ...tapasin binding / TAP complex / ABC-type peptide antigen transporter activity / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / ER-Phagosome pathway / ABC-type peptide transporter activity / antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent / Translocases; Catalysing the translocation of amino acids and peptides; Linked to the hydrolysis of a nucleoside triphosphate / peptide antigen transport / MHC class Ib protein binding / cytosol to endoplasmic reticulum transport / peptide transport / peptide transmembrane transporter activity / TAP1 binding / TAP2 binding / integral component of endoplasmic reticulum membrane / ATPase-coupled transmembrane transporter activity / MHC class I protein binding / protection from natural killer cell mediated cytotoxicity / ADP binding / peptide antigen binding / transmembrane transport / defense response / MHC class I peptide loading complex / antigen processing and presentation of endogenous peptide antigen via MHC class I / protein transport / adaptive immune response / nucleotide binding / intracellular membrane-bounded organelle / protein-containing complex binding / ATP hydrolysis activity / protein homodimerization activity / integral component of membrane / ATP binding / metal ion binding
Similarity search - Function
ABC transporter Tap-like / Antigen peptide transporter 1 / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain / ABC transporter type 1, transmembrane domain superfamily / ABC transporters family signature. / ABC transporter-like, conserved site / ABC transporter ...ABC transporter Tap-like / Antigen peptide transporter 1 / Type 1 protein exporter / ABC transporter transmembrane region / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain / ABC transporter type 1, transmembrane domain superfamily / ABC transporters family signature. / ABC transporter-like, conserved site / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Antigen peptide transporter 1
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsProcko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R.
CitationJournal: Mol.Cell / Year: 2001
Title: Distinct Structural and Functional Properties of the ATPase Sites in an Asymmetric Abc Transporter.
Authors: Procko, E. / Ferrin-O'Connell, I. / Ng, S.-L. / Gaudet, R.
History
DepositionJul 8, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANTIGEN PEPTIDE TRANSPORTER 1
B: ANTIGEN PEPTIDE TRANSPORTER 1
C: ANTIGEN PEPTIDE TRANSPORTER 1
D: ANTIGEN PEPTIDE TRANSPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,61217
Polymers118,0264
Non-polymers2,58613
Water17,439968
1
A: ANTIGEN PEPTIDE TRANSPORTER 1
B: ANTIGEN PEPTIDE TRANSPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3529
Polymers59,0132
Non-polymers1,3397
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-33.6 kcal/mol
Surface area21780 Å2
MethodPISA
2
C: ANTIGEN PEPTIDE TRANSPORTER 1
D: ANTIGEN PEPTIDE TRANSPORTER 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2608
Polymers59,0132
Non-polymers1,2476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-33.9 kcal/mol
Surface area21360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.269, 108.917, 123.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A470 - 718
2116B470 - 718
1126C470 - 718
2126D470 - 718

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.9998, 0.00385, 0.01969), (-0.00449, -0.99946, -0.03261), (0.01956, -0.03269, 0.99927)41.55157, 26.49411, -0.05401
2given(0.99725, -0.07116, 0.02047), (0.07221, 0.99581, -0.05606), (-0.0164, 0.05739, 0.99822)-2.25715, 51.8215, 1.61842
3given(-0.99755, 0.06981, -0.00404), (-0.06965, -0.99708, -0.03119), (-0.00621, -0.03084, 0.99951)43.91716, -26.04229, -2.11583

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Components

#1: Protein
ANTIGEN PEPTIDE TRANSPORTER 1 / TAP1 / APT1 / PEPTIDE TRANSPORTER TAP1 / ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 2


Mass: 29506.486 Da / Num. of mol.: 4 / Fragment: ATPASE DOMAIN, RESIDUES 465-725 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1 (TAP1)
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PET21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P36370
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 968 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 645 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLN 678 TO HIS ...ENGINEERED RESIDUE IN CHAIN A, ASP 645 TO GLN ENGINEERED RESIDUE IN CHAIN A, GLN 678 TO HIS ENGINEERED RESIDUE IN CHAIN B, ASP 645 TO GLN ENGINEERED RESIDUE IN CHAIN B, GLN 678 TO HIS ENGINEERED RESIDUE IN CHAIN C, ASP 645 TO GLN ENGINEERED RESIDUE IN CHAIN C, GLN 678 TO HIS ENGINEERED RESIDUE IN CHAIN D, ASP 645 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLN 678 TO HIS
Sequence detailsRESIDUE 464 IS THE START METHIONINE.

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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: 2.35 Å3/Da / Density % sol: 47.7 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 8
Details: HANGING DROP VAPOR DIFFUSION WITH THE RESERVOIR CONTAINING 0.75 M TRI-SODIUM CITRATE PH 8.0 .

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jan 18, 2006 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 74956 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IXE
Resolution: 2→38.49 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.935 / SU B: 7.733 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3776 5 %RANDOM
Rwork0.216 ---
obs0.218 71102 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.56 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å20 Å2
2---0.13 Å20 Å2
3---1.33 Å2
Refinement stepCycle: LAST / Resolution: 2→38.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7631 0 158 968 8757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0218066
X-RAY DIFFRACTIONr_bond_other_d0.0010.025305
X-RAY DIFFRACTIONr_angle_refined_deg1.0971.98511006
X-RAY DIFFRACTIONr_angle_other_deg0.911312964
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14651043
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.70123.658339
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.52151264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6711554
X-RAY DIFFRACTIONr_chiral_restr0.0730.21245
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021609
X-RAY DIFFRACTIONr_nbd_refined0.1840.21635
X-RAY DIFFRACTIONr_nbd_other0.1720.25672
X-RAY DIFFRACTIONr_nbtor_refined0.1660.23874
X-RAY DIFFRACTIONr_nbtor_other0.0810.24150
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2798
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.110.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.2118
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1560.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4531.56593
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.52628104
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.89133401
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.3754.52889
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3078loose positional0.265
12B3078loose positional0.265
21C3057loose positional0.275
22D3057loose positional0.275
11A3078loose thermal0.4510
12B3078loose thermal0.4510
21C3057loose thermal0.510
22D3057loose thermal0.510
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 277
Rwork0.256 5071
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.65360.41811.35332.30230.55151.75430.0936-0.1431-0.1808-0.085-0.11330.3058-0.0598-0.24140.0196-0.2058-0.02090.0103-0.12980.0613-0.1729-0.51876.2913-16.9242
23.0573-0.86571.3173.82680.36671.3725-0.01070.1120.2221-0.3582-0.10150.2235-0.1779-0.06210.1122-0.14130.0015-0.0059-0.14610.0293-0.172-2.202411.654-22.7842
36.9060.4149-0.1247.4636-0.80733.5043-0.12570.23420.1811-0.19520.08380.1679-0.1567-0.20080.042-0.1108-0.020.0167-0.2443-0.0014-0.151214.107530.6147-23.9752
41.72070.8285-0.26161.47951.09011.40840.2482-0.56130.32750.0869-0.1117-0.051-0.2278-0.1664-0.1365-0.09490.01710.0875-0.101-0.0282-0.10768.975921.0918-10.0813
52.859-0.25340.32224.4052.887210.1670.3376-0.6864-0.33930.7911-0.065-0.30780.41240.1807-0.2726-0.1067-0.08050.00170.03110.1307-0.08888.22994.9414-1.5359
63.34320.7412-0.76962.3976-0.33591.63630.0933-0.12360.1434-0.0047-0.1363-0.25290.06390.16110.043-0.1714-0.05920.0126-0.1563-0.0176-0.232341.855420.4056-17.0553
73.1422-0.9964-1.37784.4758-0.37231.435-0.01010.1711-0.1488-0.3111-0.0911-0.24770.16640.06570.1013-0.133-0.02730.038-0.1613-0.0041-0.211543.321215.3809-23.0662
86.93051.56220.05557.21411.26153.6137-0.17410.383-0.1844-0.24090.1364-0.16790.12440.17420.0377-0.1335-0.0180.0084-0.241-0.0103-0.185226.8577-3.3819-24.653
92.80670.79190.10670.8294-0.71381.89610.2256-0.5335-0.28540.1512-0.1130.07940.07180.2532-0.1125-0.1487-0.0191-0.0324-0.12860.0127-0.181432.23175.5968-10.4385
102.42770.3581-0.29875.6711-4.29978.02610.4277-0.82310.44090.7782-0.28110.5101-0.5981-0.1967-0.1466-0.0095-0.19230.03520.1043-0.1368-0.138133.726622.0823-1.3206
112.1706-0.21280.96692.32710.03662.15010.1701-0.1757-0.17650.0263-0.11230.2887-0.014-0.4017-0.0577-0.185-0.03520.0059-0.06950.0837-0.1577-1.0462-46.6217-15.9254
122.4303-2.33591.41534.7761-0.16231.39110.12060.19990.155-0.2294-0.22310.1547-0.1141-0.15010.1025-0.16040.00280.0095-0.06520.0397-0.1631-2.6583-41.1456-22.1543
139.09592.4342-0.95543.7583-0.11943.8254-0.1660.1051-0.1804-0.20160.0617-0.0017-0.0102-0.08550.1043-0.1203-0.00340.0152-0.2493-0.0052-0.140915.3192-24.0185-24.3634
145.90512.2870.0031.050.67042.72630.5114-0.66680.81030.0686-0.051-0.0094-0.4788-0.1271-0.4604-0.0451-0.01330.1646-0.0912-0.0207-0.00749.409-32.1778-9.4725
152.93890.92070.28442.75061.63228.69490.2839-0.5302-0.31990.3697-0.184-0.29110.30550.2205-0.0999-0.1107-0.10460.0060.01410.1412-0.12716.8984-48.2994-0.3823
162.36190.6291-0.7443.4341-0.55552.48680.2429-0.4170.05650.195-0.3258-0.4806-0.03410.41740.0829-0.1516-0.08310.015-0.0370.0117-0.124841.9039-34.8508-15.6909
172.5667-1.2145-1.57814.8344-0.3981.64610.1269-0.0277-0.3101-0.2116-0.3605-0.45120.10620.21570.2336-0.1627-0.01740.0361-0.06670.034-0.062443.9806-40.3457-21.7252
188.87142.36670.61023.40610.05423.3163-0.2361-0.05-0.2434-0.3126-0.0038-0.26120.11730.19690.2399-0.11250.02980.0461-0.22850.0403-0.090625.7962-57.7055-23.8411
197.24962.6765-2.00031.192-1.38712.61540.2564-1.0469-0.86630.1442-0.3131-0.20930.09090.50720.0567-0.1128-0.0047-0.06720.02370.0851-0.043131.4059-49.056-9.0309
205.72411.6309-0.86364.0274-1.66538.72450.6576-1.07350.34131.024-0.86680.3902-0.29-0.19610.20920.1085-0.30190.03340.2434-0.1131-0.13633.2933-33.2567-0.4986
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A470 - 519
2X-RAY DIFFRACTION2A520 - 564
3X-RAY DIFFRACTION3A565 - 638
4X-RAY DIFFRACTION4A639 - 683
5X-RAY DIFFRACTION5A684 - 719
6X-RAY DIFFRACTION6B470 - 519
7X-RAY DIFFRACTION7B520 - 564
8X-RAY DIFFRACTION8B565 - 638
9X-RAY DIFFRACTION9B639 - 683
10X-RAY DIFFRACTION10B684 - 719
11X-RAY DIFFRACTION11C470 - 519
12X-RAY DIFFRACTION12C520 - 564
13X-RAY DIFFRACTION13C565 - 638
14X-RAY DIFFRACTION14C639 - 683
15X-RAY DIFFRACTION15C684 - 719
16X-RAY DIFFRACTION16D470 - 519
17X-RAY DIFFRACTION17D520 - 563
18X-RAY DIFFRACTION18D566 - 638
19X-RAY DIFFRACTION19D639 - 683
20X-RAY DIFFRACTION20D684 - 719

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