4K31

Crystal structure of apramycin bound to the leishmanial rRNA A-site

> Summary

Summary for 4K31

Related4K32
Descriptor5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3'
Functional Keywordsrrna duplex, ribosomal a-site, aminoglycoside, ribosome, rna, rna-antibiotic complex, rna/antibiotic
Biological sourceLeishmania
Total number of polymer chains2
Total molecular weight16871.21
Authors
Shalev, M.,Kondo, J.,Adir, N.,Baasov, T. (deposition date: 2013-04-10, release date: 2013-07-31, modification date: 2013-09-04)
Primary citation
Shalev, M.,Kondo, J.,Kopelyanskiy, D.,Jaffe, C.L.,Adir, N.,Baasov, T.
Identification of the molecular attributes required for aminoglycoside activity against Leishmania.
Proc.Natl.Acad.Sci.USA, 110:13333-13338, 2013
PubMed: 23898171
DOI: 10.1073/pnas.1307365110
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.415 Å)
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Structure validation

RfreeClashscoreRSRZ outliersRNA backbone0.2601815.9%0.67MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4k31
no rotation
Molmil generated image of 4k31
rotated about x axis by 90°
Molmil generated image of 4k31
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
B, CRNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*GP*UP*UP*CP*CP*GP*GP*AP*AP*AP*AP*GP*UP*CP*GP*C)-3')polymer237356.42
Leishmania
APRAMYCINnon-polymer539.64
waterwater18.0209

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains2
Total molecular weight14712.9
Non-Polymers*Number of molecules4
Total molecular weight2158.3
All*Total molecular weight16871.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.415 Å)

Cell axes32.79032.790107.400
Cell angles90.0090.00120.00
SpacegroupP 31
Resolution limits19.51 - 1.42
the highest resolution shell value1.480 - 1.415
R-factor0.2277
R-work0.22580
the highest resolution shell value0.246
R-free0.26440
the highest resolution shell value0.283
RMSD bond length0.006
RMSD bond angle0.976

Data Collection Statistics

Resolution limits35.80 - 1.40
the highest resolution shell value -
Number of reflections23325
Rmerge_l_obs0.048
the highest resolution shell value0.137
Completeness94.5
Redundancy2.9
I/sigma(I)21.5

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7293.15

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
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC113BINDING SITE FOR RESIDUE AM2 B 101
ChainResidue
BC4
BG5
BU6
BG8
BHOH
BHOH
BHOH
BHOH
BHOH
CA17
CG19
CU20
CHOH

AC224BINDING SITE FOR RESIDUE AM2 B 102
ChainResidue
BU9
BU10
BC11
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
BHOH
CG8
CU9
CC23
CHOH
CHOH
CHOH
CHOH
CHOH

AC323BINDING SITE FOR RESIDUE AM2 C 101
ChainResidue
BG8
BU9
BC23
BHOH
BHOH
BHOH
CU9
CU10
CC11
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH

AC417BINDING SITE FOR RESIDUE AM2 C 102
ChainResidue
BG14
BA17
BG19
BU20
BHOH
BHOH
CC4
CG5
CU6
CG8
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH
CHOH

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

site_idNumber of ResiduesDetails
AM2_4k31_B_10112APRAMYCIN binding site
ChainResidueligand
BC4-G8AM2: APRAMYCIN
CG14AM2: APRAMYCIN
CA17-G22AM2: APRAMYCIN

AM2_4k31_C_1019APRAMYCIN binding site
ChainResidueligand
BC7-U9AM2: APRAMYCIN
CG8-G13AM2: APRAMYCIN

AM2_4k31_B_1029APRAMYCIN binding site
ChainResidueligand
BG8-G13AM2: APRAMYCIN
CC7-U9AM2: APRAMYCIN

AM2_4k31_C_10212APRAMYCIN binding site
ChainResidueligand
BG14AM2: APRAMYCIN
BA17-G22AM2: APRAMYCIN
CC4-G8AM2: APRAMYCIN

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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
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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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