1VVJ

Crystal Structure of Frameshift Suppressor tRNA SufA6 bound to Codon CCC-G on the Ribosome

This is a large structure.

> Summary

Summary for 1VVJ

Integrates4KWZ 4KX0 4KX1 4KX2
DescriptorPROTEIN/RNA Complex
Functional Keywordsprotein biosynthesis, ribosomes, rna, trna, transfer rna, 30s, 70s, 16s, 23s, ribosomal subunit, ribosome
Biological sourceThermus thermophilus
More
Total number of polymer chains110
Total molecular weight4425135.72
Authors
Maehigashi, T.,Dunkle, J.A.,Dunham, C.M. (deposition date: 2013-05-24, release date: 2014-08-06, modification date: 2014-12-10)
Primary citation
Maehigashi, T.,Dunkle, J.A.,Miles, S.J.,Dunham, C.M.
Structural insights into +1 frameshifting promoted by expanded or modification-deficient anticodon stem loops.
Proc.Natl.Acad.Sci.USA, 111:12740-12745, 2014
PubMed: 25128388
DOI: 10.1073/pnas.1409436111
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (3.44000111574 Å)
?

Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliersRNA backbone0.2843413.7%14.7%6.5%0.45MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1vvj
no rotation
Molmil generated image of 1vvj
rotated about x axis by 90°
Molmil generated image of 1vvj
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
QA, XA16S rRNApolymer1522493959.52
GenBank (AP008226)
Thermus thermophilus
QB, XB30S ribosomal protein S2polymer25629317.92
UniProt (P80371)
Pfam (PF00318)
Thermus thermophilus
QC, XC30S ribosomal protein S3polymer23926751.32
UniProt (P80372)
Pfam (PF00189)
Pfam (PF07650)
Thermus thermophilus
QD, XD30S ribosomal protein S4polymer20924373.62
UniProt (P80373)
Pfam (PF00163)
Pfam (PF01479)
Thermus thermophilus
QE, XE30S ribosomal protein S5polymer16217583.62
UniProt (Q5SHQ5)
Pfam (PF00333)
Pfam (PF03719)
Thermus thermophilus
QF, XF30S ribosomal protein S6polymer10111988.92
UniProt (Q5SLP8)
Pfam (PF01250)
Thermus thermophilus
QG, XG30S ribosomal protein S7polymer15618051.12
UniProt (P17291)
Pfam (PF00177)
Thermus thermophilus
QH, XH30S ribosomal protein S8polymer13815868.72
UniProt (Q5SHQ2)
Pfam (PF00410)
Thermus thermophilus
QI, XI30S ribosomal protein S9polymer12814410.82
UniProt (P80374)
Pfam (PF00380)
Thermus thermophilus
QJ, XJ30S ribosomal protein S10polymer10511955.12
UniProt (Q5SHN7)
Pfam (PF00338)
Thermus thermophilus
QK, XK30S ribosomal protein S11polymer12913738.02
UniProt (P80376)
Pfam (PF00411)
Thermus thermophilus
QL, XL30S ribosomal protein S12polymer13214637.52
UniProt (Q5SHN3)
Pfam (PF00164)
Thermus thermophilus
QM, XM30S ribosomal protein S13polymer12614339.02
UniProt (P80377)
Pfam (PF00416)
Thermus thermophilus
QN, XN30S ribosomal protein S14polymer617158.82
UniProt (Q5SHQ1)
Pfam (PF00253)
Thermus thermophilus
QO, XO30S ribosomal protein S15polymer8910578.52
UniProt (Q5SJ76)
Pfam (PF00312)
Thermus thermophilus
QP, XP30S ribosomal protein S16polymer8810410.12
UniProt (Q5SJH3)
Pfam (PF00886)
Thermus thermophilus
QQ, XQ30S ribosomal protein S17polymer10512325.82
UniProt (Q5SHP7)
Pfam (PF00366)
Thermus thermophilus
QR, XR30S ribosomal protein S18polymer8810258.42
UniProt (Q5SLQ0)
Pfam (PF01084)
Thermus thermophilus
QS, XS30S ribosomal protein S19polymer9310605.62
UniProt (Q5SHP2)
Pfam (PF00203)
Thermus thermophilus
QT, XT30S ribosomal protein S20polymer10611736.22
UniProt (P80380)
Pfam (PF01649)
Thermus thermophilus
QU, XU30S ribosomal protein S21polymer273350.12
UniProt (Q5SIH3)
Pfam (PF17070)
Thermus thermophilus
QV, XVP-site tRNA fMetpolymer7724802.92
GenBank (AP012306)
Escherichia coli
QX, XXA-site ASL SufA6polymer258171.12
Synthetic
QY, XYmessenger RNApolymer185818.62
Synthetic
RA, YA23S rRNApolymer2916948241.92
GenBank (AP008226)
Thermus thermophilus
RB, YB5S rRNApolymer12239494.82
GenBank (AP008226)
Thermus thermophilus
RD, YD50S ribosomal protein L2polymer27630532.82
UniProt (P60405)
Pfam (PF00181)
Pfam (PF03947)
Thermus thermophilus
RE, YE50S ribosomal protein L3polymer20622450.42
UniProt (Q5SHN8)
Pfam (PF00297)
Thermus thermophilus
RF, YF50S ribosomal protein L4polymer21023272.12
UniProt (Q5SHN9)
Pfam (PF00573)
Thermus thermophilus
RG, YG50S ribosomal protein L5polymer18221061.82
UniProt (Q5SHQ0)
Pfam (PF00281)
Pfam (PF00673)
Thermus thermophilus
RH, YH50S ribosomal protein L6polymer18019569.12
UniProt (Q5SHQ3)
Pfam (PF00347)
Thermus thermophilus
RI, YI50S ribosomal protein L9polymer14816422.32
UniProt (Q5SLQ1)
Pfam (PF01281)
Pfam (PF03948)
Thermus thermophilus
RN, YN50S ribosomal protein L13polymer14015928.02
UniProt (P60488)
Pfam (PF00572)
Thermus thermophilus
RO, YO50S ribosomal protein L14polymer12213323.72
UniProt (Q5SHP8)
Pfam (PF00238)
Thermus thermophilus
RP, YP50S ribosomal protein L15polymer15016319.32
UniProt (Q5SHQ7)
Pfam (PF00828)
Thermus thermophilus
RQ, YQ50S ribosomal protein L16polymer14115994.02
UniProt (P60489)
Pfam (PF00252)
Thermus thermophilus
RR, YR50S ribosomal protein L17polymer11813750.32
UniProt (Q9Z9H5)
Pfam (PF01196)
Thermus thermophilus
RS, YS50S ribosomal protein L18polymer11212640.02
UniProt (Q5SHQ4)
Pfam (PF00861)
Thermus thermophilus
RT, YT50S ribosomal protein L19polymer14617189.02
UniProt (P60490)
Pfam (PF01245)
Thermus thermophilus
RU, YU50S ribosomal protein L20polymer11813779.42
UniProt (P60491)
Pfam (PF00453)
Thermus thermophilus
RV, YV50S ribosomal protein L21polymer10111069.32
UniProt (P60492)
Pfam (PF00829)
Thermus thermophilus
RW, YW50S ribosomal protein L22polymer11312808.22
UniProt (Q5SHP3)
Pfam (PF00237)
Thermus thermophilus
RX, YX50S ribosomal protein L23polymer9610759.92
UniProt (Q5SHP0)
Pfam (PF00276)
Thermus thermophilus
RY, YY50S ribosomal protein L24polymer11012085.72
UniProt (Q5SHP9)
Pfam (PF00467)
Pfam (PF17136)
Thermus thermophilus
RZ, YZ50S ribosomal protein L25polymer20623238.82
UniProt (Q5SHZ1)
Pfam (PF01386)
Pfam (PF14693)
Thermus thermophilus
R0, Y050S ribosomal protein L27polymer859529.22
UniProt (P60493)
Pfam (PF01016)
Thermus thermophilus
R1, Y150S ribosomal protein L28polymer9811004.32
UniProt (P60494)
Pfam (PF00830)
Thermus thermophilus
R2, Y250S ribosomal protein L29polymer728670.32
UniProt (Q5SHP6)
Pfam (PF00831)
Thermus thermophilus
R3, Y350S ribosomal protein L30polymer606799.22
UniProt (Q5SHQ6)
Pfam (PF00327)
Thermus thermophilus
R4, Y450S ribosomal protein L32polymer718300.62
UniProt (Q5SJE1)
Pfam (PF01197)
Thermus thermophilus
R5, Y550S ribosomal protein L33polymer606722.12
UniProt (P80339)
Pfam (PF01783)
Thermus thermophilus
R6, Y650S ribosomal protein L34polymer546632.92
UniProt (P35871)
Pfam (PF00471)
Thermus thermophilus
R7, Y750S ribosomal protein L35polymer496132.52
UniProt (P80340)
Pfam (PF00468)
Thermus thermophilus
R8, Y8tRNA acceptor end mimicpolymer657506.22
UniProt (Q5SKU1)
Pfam (PF01632)
Thermus thermophilus
Z6, Z8RNA (5'-R(*CP*CP*(PPU))-3')polymer31098.92
Synthetic
MAGNESIUM IONnon-polymer24.3601
PAROMOMYCINnon-polymer615.62
ZINC IONnon-polymer65.44

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains110
Total molecular weight4409035.6
Non-Polymers*Number of molecules607
Total molecular weight16100.1
All*Total molecular weight4425135.7
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (3.44000111574 Å)

Cell axes209.546449.211619.237
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits34.81 - 3.44
the highest resolution shell value3.479 - 3.440
R-factor0.245027068825
R-work0.24315
the highest resolution shell value0.315
R-free0.28452
the highest resolution shell value0.343
RMSD bond length0.007
RMSD bond angle1.218

Data Collection Statistics

Resolution limits34.82 - 3.26
the highest resolution shell value -
Number of reflections881904
Rmerge_l_obs0.195
the highest resolution shell value0.012
Completeness98.1
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1vapor diffusion7293

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
RN0005840cellular_componentribosome
RN0003735molecular_functionstructural constituent of ribosome
RN0006412biological_processtranslation
YN0005840cellular_componentribosome
YN0003735molecular_functionstructural constituent of ribosome
YN0006412biological_processtranslation
RO0015934cellular_componentlarge ribosomal subunit
RO0019843molecular_functionrRNA binding
RO0003735molecular_functionstructural constituent of ribosome
RO0006412biological_processtranslation
YO0015934cellular_componentlarge ribosomal subunit
YO0019843molecular_functionrRNA binding
YO0003735molecular_functionstructural constituent of ribosome
YO0006412biological_processtranslation
RP0015934cellular_componentlarge ribosomal subunit
RP0019843molecular_functionrRNA binding
RP0003735molecular_functionstructural constituent of ribosome
RP0006412biological_processtranslation
YP0015934cellular_componentlarge ribosomal subunit
YP0019843molecular_functionrRNA binding
YP0003735molecular_functionstructural constituent of ribosome
YP0006412biological_processtranslation
RQ0005840cellular_componentribosome
RQ0019843molecular_functionrRNA binding
RQ0003735molecular_functionstructural constituent of ribosome
RQ0000049molecular_functiontRNA binding
RQ0006412biological_processtranslation
YQ0005840cellular_componentribosome
YQ0019843molecular_functionrRNA binding
YQ0003735molecular_functionstructural constituent of ribosome
YQ0000049molecular_functiontRNA binding
YQ0006412biological_processtranslation
RR0005840cellular_componentribosome
RR0003735molecular_functionstructural constituent of ribosome
RR0006412biological_processtranslation
YR0005840cellular_componentribosome
YR0003735molecular_functionstructural constituent of ribosome
YR0006412biological_processtranslation
RS0005840cellular_componentribosome
RS0019843molecular_functionrRNA binding
RS0003735molecular_functionstructural constituent of ribosome
RS0006412biological_processtranslation
YS0005840cellular_componentribosome
YS0019843molecular_functionrRNA binding
YS0003735molecular_functionstructural constituent of ribosome
YS0006412biological_processtranslation
RT0005840cellular_componentribosome
RT0019843molecular_functionrRNA binding
RT0003735molecular_functionstructural constituent of ribosome
RT0006412biological_processtranslation
YT0005840cellular_componentribosome
YT0019843molecular_functionrRNA binding
YT0003735molecular_functionstructural constituent of ribosome
YT0006412biological_processtranslation
RU0005840cellular_componentribosome
RU0019843molecular_functionrRNA binding
RU0003735molecular_functionstructural constituent of ribosome
RU0006412biological_processtranslation
YU0005840cellular_componentribosome
YU0019843molecular_functionrRNA binding
YU0003735molecular_functionstructural constituent of ribosome
YU0006412biological_processtranslation
RV0005840cellular_componentribosome
RV0019843molecular_functionrRNA binding
RV0003735molecular_functionstructural constituent of ribosome
RV0006412biological_processtranslation
YV0005840cellular_componentribosome
YV0019843molecular_functionrRNA binding
YV0003735molecular_functionstructural constituent of ribosome
YV0006412biological_processtranslation
RW0015934cellular_componentlarge ribosomal subunit
RW0019843molecular_functionrRNA binding
RW0003735molecular_functionstructural constituent of ribosome
RW0006412biological_processtranslation
YW0015934cellular_componentlarge ribosomal subunit
YW0019843molecular_functionrRNA binding
YW0003735molecular_functionstructural constituent of ribosome
YW0006412biological_processtranslation
RX0005840cellular_componentribosome
RX0000166molecular_functionnucleotide binding
RX0019843molecular_functionrRNA binding
RX0003735molecular_functionstructural constituent of ribosome
RX0006412biological_processtranslation
YX0005840cellular_componentribosome
YX0000166molecular_functionnucleotide binding
YX0019843molecular_functionrRNA binding
YX0003735molecular_functionstructural constituent of ribosome
YX0006412biological_processtranslation
RY0005840cellular_componentribosome
RY0019843molecular_functionrRNA binding
RY0003735molecular_functionstructural constituent of ribosome
RY0006412biological_processtranslation
YY0005840cellular_componentribosome
YY0019843molecular_functionrRNA binding
YY0003735molecular_functionstructural constituent of ribosome
YY0006412biological_processtranslation
RZ0005840cellular_componentribosome
RZ0008097molecular_function5S rRNA binding
RZ0003735molecular_functionstructural constituent of ribosome
RZ0006412biological_processtranslation
YZ0005840cellular_componentribosome
YZ0008097molecular_function5S rRNA binding
YZ0003735molecular_functionstructural constituent of ribosome
YZ0006412biological_processtranslation
R00005840cellular_componentribosome
R00003735molecular_functionstructural constituent of ribosome
R00006412biological_processtranslation
Y00005840cellular_componentribosome
Y00003735molecular_functionstructural constituent of ribosome
Y00006412biological_processtranslation
R10005840cellular_componentribosome
R10003735molecular_functionstructural constituent of ribosome
R10006412biological_processtranslation
Y10005840cellular_componentribosome
Y10003735molecular_functionstructural constituent of ribosome
Y10006412biological_processtranslation
R20005840cellular_componentribosome
R20003735molecular_functionstructural constituent of ribosome
R20006412biological_processtranslation
Y20005840cellular_componentribosome
Y20003735molecular_functionstructural constituent of ribosome
Y20006412biological_processtranslation
RD0015934cellular_componentlarge ribosomal subunit
RD0019843molecular_functionrRNA binding
RD0003735molecular_functionstructural constituent of ribosome
RD0016740molecular_functiontransferase activity
RD0006412biological_processtranslation
YD0015934cellular_componentlarge ribosomal subunit
YD0019843molecular_functionrRNA binding
YD0003735molecular_functionstructural constituent of ribosome
YD0016740molecular_functiontransferase activity
YD0006412biological_processtranslation
R30015934cellular_componentlarge ribosomal subunit
R30003735molecular_functionstructural constituent of ribosome
R30006412biological_processtranslation
Y30015934cellular_componentlarge ribosomal subunit
Y30003735molecular_functionstructural constituent of ribosome
Y30006412biological_processtranslation
R40005840cellular_componentribosome
R40046872molecular_functionmetal ion binding
R40019843molecular_functionrRNA binding
R40003735molecular_functionstructural constituent of ribosome
R40006412biological_processtranslation
Y40005840cellular_componentribosome
Y40046872molecular_functionmetal ion binding
Y40019843molecular_functionrRNA binding
Y40003735molecular_functionstructural constituent of ribosome
Y40006412biological_processtranslation
R50015934cellular_componentlarge ribosomal subunit
R50003735molecular_functionstructural constituent of ribosome
R50006412biological_processtranslation
Y50015934cellular_componentlarge ribosomal subunit
Y50003735molecular_functionstructural constituent of ribosome
Y50006412biological_processtranslation
R60005840cellular_componentribosome
R60019843molecular_functionrRNA binding
R60003735molecular_functionstructural constituent of ribosome
R60000049molecular_functiontRNA binding
R60006412biological_processtranslation
Y60005840cellular_componentribosome
Y60019843molecular_functionrRNA binding
Y60003735molecular_functionstructural constituent of ribosome
Y60000049molecular_functiontRNA binding
Y60006412biological_processtranslation
R70005840cellular_componentribosome
R70003735molecular_functionstructural constituent of ribosome
R70006412biological_processtranslation
Y70005840cellular_componentribosome
Y70003735molecular_functionstructural constituent of ribosome
Y70006412biological_processtranslation
R80005840cellular_componentribosome
R80003735molecular_functionstructural constituent of ribosome
R80006412biological_processtranslation
Y80005840cellular_componentribosome
Y80003735molecular_functionstructural constituent of ribosome
Y80006412biological_processtranslation
RE0005840cellular_componentribosome
RE0019843molecular_functionrRNA binding
RE0003735molecular_functionstructural constituent of ribosome
RE0006412biological_processtranslation
YE0005840cellular_componentribosome
YE0019843molecular_functionrRNA binding
YE0003735molecular_functionstructural constituent of ribosome
YE0006412biological_processtranslation
RF0005840cellular_componentribosome
RF0019843molecular_functionrRNA binding
RF0003735molecular_functionstructural constituent of ribosome
RF0006412biological_processtranslation
YF0005840cellular_componentribosome
YF0019843molecular_functionrRNA binding
YF0003735molecular_functionstructural constituent of ribosome
YF0006412biological_processtranslation
RG0005840cellular_componentribosome
RG0019843molecular_functionrRNA binding
RG0003735molecular_functionstructural constituent of ribosome
RG0000049molecular_functiontRNA binding
RG0006412biological_processtranslation
YG0005840cellular_componentribosome
YG0019843molecular_functionrRNA binding
YG0003735molecular_functionstructural constituent of ribosome
YG0000049molecular_functiontRNA binding
YG0006412biological_processtranslation
RI0005840cellular_componentribosome
RI0019843molecular_functionrRNA binding
RI0003735molecular_functionstructural constituent of ribosome
RI0006412biological_processtranslation
YI0005840cellular_componentribosome
YI0019843molecular_functionrRNA binding
YI0003735molecular_functionstructural constituent of ribosome
YI0006412biological_processtranslation
QJ0005840cellular_componentribosome
QJ0019843molecular_functionrRNA binding
QJ0003735molecular_functionstructural constituent of ribosome
QJ0006412biological_processtranslation
XJ0005840cellular_componentribosome
XJ0019843molecular_functionrRNA binding
XJ0003735molecular_functionstructural constituent of ribosome
XJ0006412biological_processtranslation
QK0005840cellular_componentribosome
QK0019843molecular_functionrRNA binding
QK0003735molecular_functionstructural constituent of ribosome
QK0006412biological_processtranslation
XK0005840cellular_componentribosome
XK0019843molecular_functionrRNA binding
XK0003735molecular_functionstructural constituent of ribosome
XK0006412biological_processtranslation
QL0015935cellular_componentsmall ribosomal subunit
QL0019843molecular_functionrRNA binding
QL0003735molecular_functionstructural constituent of ribosome
QL0000049molecular_functiontRNA binding
QL0006412biological_processtranslation
XL0015935cellular_componentsmall ribosomal subunit
XL0019843molecular_functionrRNA binding
XL0003735molecular_functionstructural constituent of ribosome
XL0000049molecular_functiontRNA binding
XL0006412biological_processtranslation
QM0005840cellular_componentribosome
QM0019843molecular_functionrRNA binding
QM0003735molecular_functionstructural constituent of ribosome
QM0000049molecular_functiontRNA binding
QM0006412biological_processtranslation
XM0005840cellular_componentribosome
XM0019843molecular_functionrRNA binding
XM0003735molecular_functionstructural constituent of ribosome
XM0000049molecular_functiontRNA binding
XM0006412biological_processtranslation
QO0005840cellular_componentribosome
QO0019843molecular_functionrRNA binding
QO0003735molecular_functionstructural constituent of ribosome
QO0006412biological_processtranslation
XO0005840cellular_componentribosome
XO0019843molecular_functionrRNA binding
XO0003735molecular_functionstructural constituent of ribosome
XO0006412biological_processtranslation
QP0005840cellular_componentribosome
QP0003735molecular_functionstructural constituent of ribosome
QP0006412biological_processtranslation
XP0005840cellular_componentribosome
XP0003735molecular_functionstructural constituent of ribosome
XP0006412biological_processtranslation
QR0005840cellular_componentribosome
QR0019843molecular_functionrRNA binding
QR0003735molecular_functionstructural constituent of ribosome
QR0006412biological_processtranslation
XR0005840cellular_componentribosome
XR0019843molecular_functionrRNA binding
XR0003735molecular_functionstructural constituent of ribosome
XR0006412biological_processtranslation
QS0015935cellular_componentsmall ribosomal subunit
QS0019843molecular_functionrRNA binding
QS0003735molecular_functionstructural constituent of ribosome
QS0006412biological_processtranslation
XS0015935cellular_componentsmall ribosomal subunit
XS0019843molecular_functionrRNA binding
XS0003735molecular_functionstructural constituent of ribosome
XS0006412biological_processtranslation
QT0005840cellular_componentribosome
QT0019843molecular_functionrRNA binding
QT0003735molecular_functionstructural constituent of ribosome
QT0006412biological_processtranslation
XT0005840cellular_componentribosome
XT0019843molecular_functionrRNA binding
XT0003735molecular_functionstructural constituent of ribosome
XT0006412biological_processtranslation
QB0015935cellular_componentsmall ribosomal subunit
QB0019843molecular_functionrRNA binding
QB0003735molecular_functionstructural constituent of ribosome
QB0006412biological_processtranslation
XB0015935cellular_componentsmall ribosomal subunit
XB0019843molecular_functionrRNA binding
XB0003735molecular_functionstructural constituent of ribosome
XB0006412biological_processtranslation
QC0015935cellular_componentsmall ribosomal subunit
QC0019843molecular_functionrRNA binding
QC0003735molecular_functionstructural constituent of ribosome
QC0006412biological_processtranslation
XC0015935cellular_componentsmall ribosomal subunit
XC0019843molecular_functionrRNA binding
XC0003735molecular_functionstructural constituent of ribosome
XC0006412biological_processtranslation
QD0015935cellular_componentsmall ribosomal subunit
QD0046872molecular_functionmetal ion binding
QD0019843molecular_functionrRNA binding
QD0003735molecular_functionstructural constituent of ribosome
QD0006412biological_processtranslation
XD0015935cellular_componentsmall ribosomal subunit
XD0046872molecular_functionmetal ion binding
XD0019843molecular_functionrRNA binding
XD0003735molecular_functionstructural constituent of ribosome
XD0006412biological_processtranslation
QE0015935cellular_componentsmall ribosomal subunit
QE0019843molecular_functionrRNA binding
QE0003735molecular_functionstructural constituent of ribosome
QE0006412biological_processtranslation
XE0015935cellular_componentsmall ribosomal subunit
XE0019843molecular_functionrRNA binding
XE0003735molecular_functionstructural constituent of ribosome
XE0006412biological_processtranslation
QF0005840cellular_componentribosome
QF0019843molecular_functionrRNA binding
QF0003735molecular_functionstructural constituent of ribosome
QF0006412biological_processtranslation
XF0005840cellular_componentribosome
XF0019843molecular_functionrRNA binding
XF0003735molecular_functionstructural constituent of ribosome
XF0006412biological_processtranslation
QG0015935cellular_componentsmall ribosomal subunit
QG0019843molecular_functionrRNA binding
QG0003735molecular_functionstructural constituent of ribosome
QG0000049molecular_functiontRNA binding
QG0006412biological_processtranslation
XG0015935cellular_componentsmall ribosomal subunit
XG0019843molecular_functionrRNA binding
XG0003735molecular_functionstructural constituent of ribosome
XG0000049molecular_functiontRNA binding
XG0006412biological_processtranslation
QI0005840cellular_componentribosome
QI0019843molecular_functionrRNA binding
QI0003735molecular_functionstructural constituent of ribosome
QI0000049molecular_functiontRNA binding
QI0006412biological_processtranslation
XI0005840cellular_componentribosome
XI0019843molecular_functionrRNA binding
XI0003735molecular_functionstructural constituent of ribosome
XI0000049molecular_functiontRNA binding
XI0006412biological_processtranslation
QU0005840cellular_componentribosome
QU0019843molecular_functionrRNA binding
XU0005840cellular_componentribosome
XU0019843molecular_functionrRNA binding
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
10
ChainResidue

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
PAR_1vvj_QA_166114PAROMOMYCIN binding site
ChainResidueligand
QAC1404-C1409PAR: PAROMOMYCIN
QAG1489-C1496PAR: PAROMOMYCIN

PAR_1vvj_XA_166414PAROMOMYCIN binding site
ChainResidueligand
XAC1404-C1409PAR: PAROMOMYCIN
XAG1489-C1496PAR: PAROMOMYCIN

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

Sequence navigator - 1vvj: Chain QA,XA
Sequence navigator - 1vvj: Chain QB,XB
Sequence navigator - 1vvj: Chain QC,XC
Sequence navigator - 1vvj: Chain QD,XD
Sequence navigator - 1vvj: Chain QE,XE
Sequence navigator - 1vvj: Chain QF,XF
Sequence navigator - 1vvj: Chain QG,XG
Sequence navigator - 1vvj: Chain QH,XH
Sequence navigator - 1vvj: Chain QI,XI
Sequence navigator - 1vvj: Chain QJ,XJ
Sequence navigator - 1vvj: Chain QK,XK
Sequence navigator - 1vvj: Chain QL,XL
Sequence navigator - 1vvj: Chain QM,XM
Sequence navigator - 1vvj: Chain QN,XN
Sequence navigator - 1vvj: Chain QO,XO
Sequence navigator - 1vvj: Chain QP,XP
Sequence navigator - 1vvj: Chain QQ,XQ
Sequence navigator - 1vvj: Chain QR,XR
Sequence navigator - 1vvj: Chain QS,XS
Sequence navigator - 1vvj: Chain QT,XT
Sequence navigator - 1vvj: Chain QU,XU
Sequence navigator - 1vvj: Chain QV,XV
Sequence navigator - 1vvj: Chain QX,XX
Sequence navigator - 1vvj: Chain QY,XY
Sequence navigator - 1vvj: Chain RA,YA
Sequence navigator - 1vvj: Chain RB,YB
Sequence navigator - 1vvj: Chain RD,YD
Sequence navigator - 1vvj: Chain RE,YE
Sequence navigator - 1vvj: Chain RF,YF
Sequence navigator - 1vvj: Chain RG,YG
Sequence navigator - 1vvj: Chain RH,YH
Sequence navigator - 1vvj: Chain RI,YI
Sequence navigator - 1vvj: Chain RN,YN
Sequence navigator - 1vvj: Chain RO,YO
Sequence navigator - 1vvj: Chain RP,YP
Sequence navigator - 1vvj: Chain RQ,YQ
Sequence navigator - 1vvj: Chain RR,YR
Sequence navigator - 1vvj: Chain RS,YS
Sequence navigator - 1vvj: Chain RT,YT
Sequence navigator - 1vvj: Chain RU,YU
Sequence navigator - 1vvj: Chain RV,YV
Sequence navigator - 1vvj: Chain RW,YW
Sequence navigator - 1vvj: Chain RX,YX
Sequence navigator - 1vvj: Chain RY,YY
Sequence navigator - 1vvj: Chain RZ,YZ
Sequence navigator - 1vvj: Chain R0,Y0
Sequence navigator - 1vvj: Chain R1,Y1
Sequence navigator - 1vvj: Chain R2,Y2
Sequence navigator - 1vvj: Chain R3,Y3
Sequence navigator - 1vvj: Chain R4,Y4
Sequence navigator - 1vvj: Chain R5,Y5
Sequence navigator - 1vvj: Chain R6,Y6
Sequence navigator - 1vvj: Chain R7,Y7
Sequence navigator - 1vvj: Chain R8,Y8
Sequence navigator - 1vvj: Chain Z6,Z8

> Downloads

Resources

File formatFile name (file size)
PDB Bundle1vvj-pdb-bundle.tar.gz (4.95 MB)
PDBx/mmCIF1vvj.cif.gz (6.62 MB)
PDBMLall1vvj.xml.gz (10.2 MB)
no-atom1vvj-noatom.xml.gz (1.36 MB)
Display
ext-atom1vvj-extatom.xml.gz (5.68 MB)
PDBMLplusall1vvj-plus.xml.gz (10.21 MB)
no-atom1vvj-plus-noatom.xml.gz (1.37 MB)
Display
add only1vvj-add.xml.gz (8.78 KB)
Display
RDF1vvj.rdf.gz (2.24 MB)
Display
Structure factorsr1vvjsf.ent.gz (7.6 MB)
Biological unit (mmCIF format)1vvj-assembly1.cif.gz (3.34 MB) (QA,QB,QC,QD,QE,...)
*author defined assembly, 55 molecule(s) (55-meric)
Display
1vvj-assembly2.cif.gz (3.36 MB) (XA,XB,XC,XD,XE,...)
*author defined assembly, 55 molecule(s) (55-meric)
Display
Validation reportsPDF1vvj​_validation.pdf.gz (1.84 MB)
Display
PDF-full1vvj​_full​_validation.pdf.gz (3.66 MB)
Display
XML1vvj​_validation.xml.gz (849.69 KB)
Display
PNG1vvj​_multipercentile​_validation.png.gz (160.81 KB)
Display
SVG1vvj​_multipercentile​_validation.svg.gz (1008 B)
Display
Sequence (fasta)1vvj​_seq.txt
Display

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