RNA 3D Hub //

Equivalence class NR_2.5_55755.1 Current

#IFEStandardized nameMoleculeOrganismSourceRfamTitleMethodRes. Å#NTsDate
17K98|1|C (rep)Transfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Preaminoacylation complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine (F-AMS)X-ray diffraction2.19772021-05-12
27K98|1|FTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Preaminoacylation complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine (F-AMS)X-ray diffraction2.19772021-05-12
39DSX|1|CTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00107555X-ray diffraction2.05732025-06-04
49DTF|1|CTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD01008876X-ray diffraction2.45732025-06-04
59DRS|1|CTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116X-ray diffraction2.35712025-02-12
69DRV|1|CTransfer RNAtRNA(phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-004X-ray diffraction2.46712025-02-12
77KA0|1|CTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and phenylalanineX-ray diffraction2.4662021-05-12
89DSX|1|FTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00107555X-ray diffraction2.05732025-06-04
97K9M|1|CTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosineX-ray diffraction2.5662021-05-12
109DTF|1|FTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD01008876X-ray diffraction2.45732025-06-04
119DRV|1|FTransfer RNAtRNA(phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-004X-ray diffraction2.46712025-02-12
129DRS|1|FTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116X-ray diffraction2.35712025-02-12
137KAB|1|CTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005M. tuberculosis PheRS complex with cognate precursor tRNA and phenylalanineX-ray diffraction2.5662021-05-12
147KA0|1|FTransfer RNAtRNA(Phe)Mycobacterium tuberculosis H37RvBacteriaRF00005Crystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and phenylalanineX-ray diffraction2.4662021-05-12

Release history

Release3.3903.3913.392
Date2025-06-042025-06-112025-06-18

Parents

This classParent classesRelease idIntersectionAdded to this classOnly in parent

Children

This class Descendant classesRelease idIntersectionOnly in this classAdded to child

Instances are ordered to put similar structures near each other. Select one instance to see its 3D structure. Selecting two or more instances will show their superposition, but only chains with identical numbers of observed nucleotides will superpose well. Large structures are slow to display; this tool is not designed for that.

#SViewPDBTitleMethodResolution#NTs
19DRV|1|FCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-004X-RAY DIFFRACTION2.4671
29DSX|1|FCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00107555X-RAY DIFFRACTION2.0573
39DTF|1|FCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD01008876X-RAY DIFFRACTION2.4573
49DTF|1|CCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD01008876X-RAY DIFFRACTION2.4573
59DRV|1|CCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-004X-RAY DIFFRACTION2.4671
69DSX|1|CCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and fragment DDD00107555X-RAY DIFFRACTION2.0573
79DRS|1|CCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116X-RAY DIFFRACTION2.3571
89DRS|1|FCrystal structure of M. tuberculosis PheRS-tRNA complex bound to inhibitor D-116X-RAY DIFFRACTION2.3571
97K98|1|FPreaminoacylation complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine (F-AMS)X-RAY DIFFRACTION2.1977
107K98|1|CPreaminoacylation complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosine (F-AMS)X-RAY DIFFRACTION2.1977
117KAB|1|CM. tuberculosis PheRS complex with cognate precursor tRNA and phenylalanineX-RAY DIFFRACTION2.566
127K9M|1|CCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and 5'-O-(N-phenylalanyl)sulfamoyl-adenosineX-RAY DIFFRACTION2.566
137KA0|1|CCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and phenylalanineX-RAY DIFFRACTION2.466
147KA0|1|FCrystal structure of the complex of M. tuberculosis PheRS with cognate precursor tRNA and phenylalanineX-RAY DIFFRACTION2.466

Heat map of mutual geometric discrepancy, in Angstroms per nucleotide. The ordering in the heat map is the same as in the table. The colorbar ranges from 0 to the maximum observed discrepancy. Click above the diagonal to select a range of structures, below the diagonal to select two structures.

9DRV|1|F:9DRV|1|F = 09DRV|1|F:9DSX|1|F = 0.09819DRV|1|F:9DTF|1|F = 0.10159DRV|1|F:9DTF|1|C = 0.12489DRV|1|F:9DRV|1|C = 0.12359DRV|1|F:9DSX|1|C = 0.12609DRV|1|F:9DRS|1|C = 0.12889DRV|1|F:9DRS|1|F = 0.14749DRV|1|F:7K98|1|F = 0.25419DRV|1|F:7K98|1|C = 0.25509DRV|1|F:7KAB|1|C = 0.31819DRV|1|F:7K9M|1|C = 0.33179DRV|1|F:7KA0|1|C = 0.33979DRV|1|F:7KA0|1|F = 0.33369DSX|1|F:9DRV|1|F = 0.09819DSX|1|F:9DSX|1|F = 09DSX|1|F:9DTF|1|F = 0.05379DSX|1|F:9DTF|1|C = 0.09479DSX|1|F:9DRV|1|C = 0.07199DSX|1|F:9DSX|1|C = 0.07129DSX|1|F:9DRS|1|C = 0.07449DSX|1|F:9DRS|1|F = 0.13309DSX|1|F:7K98|1|F = 0.23729DSX|1|F:7K98|1|C = 0.23829DSX|1|F:7KAB|1|C = 0.30499DSX|1|F:7K9M|1|C = 0.31759DSX|1|F:7KA0|1|C = 0.32609DSX|1|F:7KA0|1|F = 0.31829DTF|1|F:9DRV|1|F = 0.10159DTF|1|F:9DSX|1|F = 0.05379DTF|1|F:9DTF|1|F = 09DTF|1|F:9DTF|1|C = 0.08599DTF|1|F:9DRV|1|C = 0.08179DTF|1|F:9DSX|1|C = 0.08309DTF|1|F:9DRS|1|C = 0.08979DTF|1|F:9DRS|1|F = 0.14239DTF|1|F:7K98|1|F = 0.25079DTF|1|F:7K98|1|C = 0.25259DTF|1|F:7KAB|1|C = 0.30599DTF|1|F:7K9M|1|C = 0.31829DTF|1|F:7KA0|1|C = 0.32539DTF|1|F:7KA0|1|F = 0.31649DTF|1|C:9DRV|1|F = 0.12489DTF|1|C:9DSX|1|F = 0.09479DTF|1|C:9DTF|1|F = 0.08599DTF|1|C:9DTF|1|C = 09DTF|1|C:9DRV|1|C = 0.04459DTF|1|C:9DSX|1|C = 0.07079DTF|1|C:9DRS|1|C = 0.05959DTF|1|C:9DRS|1|F = 0.14949DTF|1|C:7K98|1|F = 0.24259DTF|1|C:7K98|1|C = 0.24079DTF|1|C:7KAB|1|C = 0.28239DTF|1|C:7K9M|1|C = 0.29779DTF|1|C:7KA0|1|C = 0.30579DTF|1|C:7KA0|1|F = 0.29879DRV|1|C:9DRV|1|F = 0.12359DRV|1|C:9DSX|1|F = 0.07199DRV|1|C:9DTF|1|F = 0.08179DRV|1|C:9DTF|1|C = 0.04459DRV|1|C:9DRV|1|C = 09DRV|1|C:9DSX|1|C = 0.03369DRV|1|C:9DRS|1|C = 0.04089DRV|1|C:9DRS|1|F = 0.14589DRV|1|C:7K98|1|F = 0.23179DRV|1|C:7K98|1|C = 0.22619DRV|1|C:7KAB|1|C = 0.28579DRV|1|C:7K9M|1|C = 0.30049DRV|1|C:7KA0|1|C = 0.30879DRV|1|C:7KA0|1|F = 0.30319DSX|1|C:9DRV|1|F = 0.12609DSX|1|C:9DSX|1|F = 0.07129DSX|1|C:9DTF|1|F = 0.08309DSX|1|C:9DTF|1|C = 0.07079DSX|1|C:9DRV|1|C = 0.03369DSX|1|C:9DSX|1|C = 09DSX|1|C:9DRS|1|C = 0.05219DSX|1|C:9DRS|1|F = 0.15089DSX|1|C:7K98|1|F = 0.23649DSX|1|C:7K98|1|C = 0.23449DSX|1|C:7KAB|1|C = 0.28099DSX|1|C:7K9M|1|C = 0.29379DSX|1|C:7KA0|1|C = 0.30289DSX|1|C:7KA0|1|F = 0.29799DRS|1|C:9DRV|1|F = 0.12889DRS|1|C:9DSX|1|F = 0.07449DRS|1|C:9DTF|1|F = 0.08979DRS|1|C:9DTF|1|C = 0.05959DRS|1|C:9DRV|1|C = 0.04089DRS|1|C:9DSX|1|C = 0.05219DRS|1|C:9DRS|1|C = 09DRS|1|C:9DRS|1|F = 0.13149DRS|1|C:7K98|1|F = 0.21669DRS|1|C:7K98|1|C = 0.21179DRS|1|C:7KAB|1|C = 0.28639DRS|1|C:7K9M|1|C = 0.30069DRS|1|C:7KA0|1|C = 0.30919DRS|1|C:7KA0|1|F = 0.30429DRS|1|F:9DRV|1|F = 0.14749DRS|1|F:9DSX|1|F = 0.13309DRS|1|F:9DTF|1|F = 0.14239DRS|1|F:9DTF|1|C = 0.14949DRS|1|F:9DRV|1|C = 0.14589DRS|1|F:9DSX|1|C = 0.15089DRS|1|F:9DRS|1|C = 0.13149DRS|1|F:9DRS|1|F = 09DRS|1|F:7K98|1|F = 0.16819DRS|1|F:7K98|1|C = 0.17209DRS|1|F:7KAB|1|C = 0.29969DRS|1|F:7K9M|1|C = 0.31389DRS|1|F:7KA0|1|C = 0.32009DRS|1|F:7KA0|1|F = 0.31647K98|1|F:9DRV|1|F = 0.25417K98|1|F:9DSX|1|F = 0.23727K98|1|F:9DTF|1|F = 0.25077K98|1|F:9DTF|1|C = 0.24257K98|1|F:9DRV|1|C = 0.23177K98|1|F:9DSX|1|C = 0.23647K98|1|F:9DRS|1|C = 0.21667K98|1|F:9DRS|1|F = 0.16817K98|1|F:7K98|1|F = 07K98|1|F:7K98|1|C = 0.04567K98|1|F:7KAB|1|C = 0.28017K98|1|F:7K9M|1|C = 0.29977K98|1|F:7KA0|1|C = 0.29477K98|1|F:7KA0|1|F = 0.29727K98|1|C:9DRV|1|F = 0.25507K98|1|C:9DSX|1|F = 0.23827K98|1|C:9DTF|1|F = 0.25257K98|1|C:9DTF|1|C = 0.24077K98|1|C:9DRV|1|C = 0.22617K98|1|C:9DSX|1|C = 0.23447K98|1|C:9DRS|1|C = 0.21177K98|1|C:9DRS|1|F = 0.17207K98|1|C:7K98|1|F = 0.04567K98|1|C:7K98|1|C = 07K98|1|C:7KAB|1|C = 0.27447K98|1|C:7K9M|1|C = 0.29207K98|1|C:7KA0|1|C = 0.28747K98|1|C:7KA0|1|F = 0.29197KAB|1|C:9DRV|1|F = 0.31817KAB|1|C:9DSX|1|F = 0.30497KAB|1|C:9DTF|1|F = 0.30597KAB|1|C:9DTF|1|C = 0.28237KAB|1|C:9DRV|1|C = 0.28577KAB|1|C:9DSX|1|C = 0.28097KAB|1|C:9DRS|1|C = 0.28637KAB|1|C:9DRS|1|F = 0.29967KAB|1|C:7K98|1|F = 0.28017KAB|1|C:7K98|1|C = 0.27447KAB|1|C:7KAB|1|C = 07KAB|1|C:7K9M|1|C = 0.09867KAB|1|C:7KA0|1|C = 0.08697KAB|1|C:7KA0|1|F = 0.10767K9M|1|C:9DRV|1|F = 0.33177K9M|1|C:9DSX|1|F = 0.31757K9M|1|C:9DTF|1|F = 0.31827K9M|1|C:9DTF|1|C = 0.29777K9M|1|C:9DRV|1|C = 0.30047K9M|1|C:9DSX|1|C = 0.29377K9M|1|C:9DRS|1|C = 0.30067K9M|1|C:9DRS|1|F = 0.31387K9M|1|C:7K98|1|F = 0.29977K9M|1|C:7K98|1|C = 0.29207K9M|1|C:7KAB|1|C = 0.09867K9M|1|C:7K9M|1|C = 07K9M|1|C:7KA0|1|C = 0.07917K9M|1|C:7KA0|1|F = 0.12757KA0|1|C:9DRV|1|F = 0.33977KA0|1|C:9DSX|1|F = 0.32607KA0|1|C:9DTF|1|F = 0.32537KA0|1|C:9DTF|1|C = 0.30577KA0|1|C:9DRV|1|C = 0.30877KA0|1|C:9DSX|1|C = 0.30287KA0|1|C:9DRS|1|C = 0.30917KA0|1|C:9DRS|1|F = 0.32007KA0|1|C:7K98|1|F = 0.29477KA0|1|C:7K98|1|C = 0.28747KA0|1|C:7KAB|1|C = 0.08697KA0|1|C:7K9M|1|C = 0.07917KA0|1|C:7KA0|1|C = 07KA0|1|C:7KA0|1|F = 0.11067KA0|1|F:9DRV|1|F = 0.33367KA0|1|F:9DSX|1|F = 0.31827KA0|1|F:9DTF|1|F = 0.31647KA0|1|F:9DTF|1|C = 0.29877KA0|1|F:9DRV|1|C = 0.30317KA0|1|F:9DSX|1|C = 0.29797KA0|1|F:9DRS|1|C = 0.30427KA0|1|F:9DRS|1|F = 0.31647KA0|1|F:7K98|1|F = 0.29727KA0|1|F:7K98|1|C = 0.29197KA0|1|F:7KAB|1|C = 0.10767KA0|1|F:7K9M|1|C = 0.12757KA0|1|F:7KA0|1|C = 0.11067KA0|1|F:7KA0|1|F = 09DRV|1|F9DSX|1|F9DTF|1|F9DTF|1|C9DRV|1|C9DSX|1|C9DRS|1|C9DRS|1|F7K98|1|F7K98|1|C7KAB|1|C7K9M|1|C7KA0|1|C7KA0|1|FDiscrepancy0.000.050.100.150.200.250.30

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