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1vq8

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Warning: this is a large structure, and loading might take a long time or not happen at all.

1vq8, resolution 2.20Å (default scene)

Ligands:

CD, CL, K, MG, NA, SPS, SR

Non-Standard Residues:

1MA, ACA, OMG, OMU, PSU, UR3

Related:

1s72, 1jj2, 1kqs, 1m90, 1q7y, 1q81, 1q82, 1q86, 1qvf, 1qvg, 1ffk, 1ffz, 1fgo, 1vq4, 1vq5, 1vq6, 1vq7, 1vq9, 1vqk, 1vql, 1vqm, 1vqn, 1vqo, 1vqp

Structural annotation:

Resources:

CATH : 1Vq8100, 1Vq8200, 1Vq8300, 1Vq8A02, 1Vq8A01, 1Vq8A03, 1Vq8B01, 1Vq8B02, 1Vq8B03, 1Vq8C00, 1Vq8D00, 1Vq8E02, 1Vq8E01, 1Vq8F00, 1Vq8H00, 1Vq8I00, 1Vq8J00, 1Vq8K00, 1Vq8L02, 1Vq8L01, 1Vq8M00, 1Vq8N00, 1Vq8O00, 1Vq8P01, 1Vq8P03, 1Vq8P02, 1Vq8Q00, 1Vq8R00, 1Vq8S00, 1Vq8T00, 1Vq8U00, 1Vq8V00, 1Vq8W01, 1Vq8W02, 1Vq8X00, 1Vq8Z00
InterPro : Ipr011331, Ipr001569, Ipr011332, Ipr000077, Ipr000552, Ipr014726, Ipr002171, Ipr008991, Ipr012340, Ipr009000, Ipr000597, Ipr002048, Ipr002136, Ipr013000, Ipr002132, Ipr002359, Ipr000702, Ipr000948, Ipr004037, Ipr004038, Ipr013522, Ipr001790, Ipr001197, Ipr000911, Ipr005755, Ipr005822, Ipr000218, Ipr001196, Ipr012678, Ipr000439, Ipr005484, Ipr005485, Ipr000039, Ipr000196, Ipr001147, Ipr001063, Ipr005721, Ipr001014, Ipr012677, Ipr013025, Ipr005756, Ipr005825, Ipr014723, Ipr005824, Ipr000988, Ipr011017, Ipr001854, Ipr000517, Ipr005997, Ipr000054, Ipr001515, Ipr010995, Ipr003583, Ipr002674
Pfam : PF01907, PF00832, PF00935, PF03947, PF00181, PF00297, PF00573, PF00281, PF00673, PF00347, PF01248, PF00466, PF00826, PF03946, PF00298, PF00572, PF00238, PF00256, PF00827, PF00861, PF01280, PF01157, PF00237, PF00276, PF00467, PF01246, PF00831, PF00327, PF01198, PF01655, PF01780
UniProt : P32410, P22452, P32411, P20276, P20279, P12735, P14124, P14135, P12743, P15825, P60617, P14122, P29198, P22450, P12737, P60618, P14123, P12733, P14119, P12734, P10970, P12732, P10972, P14116, P10971, P14121, P18138, P12736, P60619

Functional annotation:
Cellular component:	intracellular ribosome ribonucleoprotein complex large ribosomal subunit
Biological process:	translation ribosome biogenesis and assembly
Molecular function:	structural constituent of ribosome RNA binding rRNA binding metal ion binding zinc ion binding tRNA binding 5S rRNA binding nucleotide binding sequence-specific DNA binding protein binding

Evolutionary conservation:

Toggle Conservation Colors:

Rows = identical sequences:

Further Information:

Caveats,

Explanation,
Complete Results at ConSurfDB

Resources:

FirstGlance, OCA, RCSB, PDBsum

Coordinates:

save as pdb, mmCIF, xml

1 The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui
2 About this Structure
3 See Also
4 Reference

The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui

Publication Abstract from PubMed

Peptide bond formation is catalyzed at the peptidyl transferase center (PTC) of the large ribosomal subunit. Crystal structures of the large ribosomal subunit of Haloarcula marismortui (Hma) complexed with several analogs that represent either the substrates or the transition state intermediate of the peptidyl transferase reaction show that this reaction proceeds through a tetrahedral intermediate with S chirality. The oxyanion of the tetrahedral intermediate interacts with a water molecule that is positioned by nucleotides A2637 (E. coli numbering, 2602) and (methyl)U2619(2584). There are no Mg2+ ions or monovalent metal ions observed in the PTC that could directly promote catalysis. The A76 2' hydroxyl of the peptidyl-tRNA is hydrogen bonded to the alpha-amino group and could facilitate peptide bond formation by substrate positioning and by acting as a proton shuttle between the alpha-amino group and the A76 3' hydroxyl of the peptidyl-tRNA.

Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction., Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA, Mol Cell. 2005 Nov 11;20(3):437-48. PMID:16285925

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

About this Structure

1vq8 is a 31 chain structure with sequence from Haloarcula marismortui. Full crystallographic information is available from OCA.

Reference

Schmeing TM, Huang KS, Kitchen DE, Strobel SA, Steitz TA. Structural insights into the roles of water and the 2' hydroxyl of the P site tRNA in the peptidyl transferase reaction. Mol Cell. 2005 Nov 11;20(3):437-48. PMID:16285925 doi:10.1016/j.molcel.2005.09.006

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1vq8

From Proteopedia

Contents

The structure of CCDA-PHE-CAP-BIO and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui

About this Structure

See Also

Reference

Proteopedia Page Contributors and Editors (what is this?)

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