1NYL: Unliganded glutaminyl-tRNA synthetase

Unliganded glutaminyl-tRNA synthetase. Determined by X-ray diffraction at 2.6 Å resolution. Released 25 Feb 2003.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Escherichia coli
Chains: 1
Atoms: 4,240
Mol. weight: 61.92 kDa
Released: 25 Feb 2003

Explore 1NYL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1NYL contains 18 α-helices and 36 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 18 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	10-20	11
β-strand	28-31	4	1
β-strand	40	1	2
α-helix	41-56	16
β-strand	60-63	4	1
β-strand	64-65	2	3
α-helix	77-88	12
β-strand	97-98	2	3
α-helix	99-102	4
α-helix	103-115	13
β-strand	119-122	4	4
α-helix	126-132	7
α-helix	150-162	13
β-strand	171-174	4	4
α-helix	183-185	3
β-strand	189-193	5	4
β-strand	207-209	3	4
α-helix	211-222	12
β-strand	226-230	5	5
α-helix	231-233	3
α-helix	236-246	11
β-strand	254-258	5	5
α-helix	259-261	3
β-strand	263	1	6
α-helix	270-277	8
β-strand	292	1	2
α-helix	293-299	7
α-helix	303-310	8
β-strand	322	1	6
α-helix	324-338	15
β-strand	341-342	2	7
β-strand	344-345	2	7
β-strand	348-353	6	8
β-strand	360-364	5	9
β-strand	378-382	5	9
β-strand	384-388	5	8
α-helix	389-391	3
β-strand	392	1	10
β-strand	403	1	10
β-strand	410	1	11
β-strand	411	1	12
β-strand	416	1	11
β-strand	419-423	5	8
β-strand	432-435	4	8
β-strand	456	1	12
β-strand	459-460	2	8
β-strand	465-471	7	7
β-strand	476	1	13
β-strand	491	1	13
β-strand	497-503	7	7
α-helix	505-508	4
β-strand	515-518	4	7
β-strand	522-526	5	7
β-strand	537-542	6	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Glutaminyl-tRNA synthetase	A	protein	539	Escherichia coli	P00962 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1NYL_1 Glutaminyl-tRNA synthetase (chains A)
TNFIRQIIDEDLASGKHTTVHTRFPPEPNGYLHIGHAKSICLNFGIAQDYKGQCNLRFDD
TNPVKEDIEYVESIKNDVEWLGFHWSGNVRYSSDYFDQLHAYAIELINKGLAYVDELTPE
QIREYRGTLTQPGKNSPYRDRSVEENLALFEKMRAGGFEEGKACLRAKIDMASPFIVMRD
PVLYRIKFAEHHQTGNKWCIYPMYDFTHCISDALEGITHSLCTLEFQDNRRLYDWVLDNI
TIPVHPRQYEFSRLNLEYTVMSKRKLNLLVTDKHVEGWDDPRMPTISGLRRRGYTAASIR
EFCKRIGVTKQDNTIEMASLESCIREDLNENAPRAMAVIDPVKLVIENYQGEGEMVTMPN
HPNKPEMGSRQVPFSGEIWIDRADFREEANKQYKRLVLGKEVRLRNAYVIKAERVEKDAE
GNITTIFCTYDADTLSKDPADGRKVKGVIHWVSAAHALPVEIRLYDRLFSVPNPGAADDF
LSVINPESLVIKQGFAEPSLKDAVAGKAFQFEREGYFCLDSRHSTAEKPVFNRTVGLRD

Primary citation

tRNA-Dependent Active Site Assembly in a Class I Aminoacyl-tRNA Synthetase. Sherlin, L.D., Perona, J.J. Structure (2003) 11:591-603. DOI 10.1016/S0969-2126(03)00074-1 · PubMed

Other PDB entries of the same protein (UniProt P00962 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1QTQ 2.25 Å, Glutaminyl-tRNA synthetase complexed with tRNA and an amino acid analog
4JXX 2.3 Å, Crystal structure of E coli E. coli glutaminyl-tRNA synthetase bound to tRNA(Gln)(CUG)…
4JXZ 2.4 Å, Structure of E. coli glutaminyl-tRNA synthetase bound to ATP and a tRNA(Gln) acceptor…
1GTR 2.5 Å, Structural basis of anticodon loop recognition by glutaminyl-tRNA synthetase
1ZJW 2.5 Å, Glutaminyl-tRNA synthetase complexed to glutamine and 2'deoxy A76 glutamine tRNA
4JYZ 2.5 Å, Crystal structure of E. coli glutaminyl-tRNA synthetase bound to ATP and native…
1EUY 2.6 Å, Glutaminyl-tRNA synthetase complexed with a tRNA mutant and an active site inhibitor
1QRS 2.6 Å, Glutaminyl-tRNA synthetase mutant D235N complexed with glutamine transfer RNA
2RD2 2.6 Å, Glutaminyl-tRNA synthetase mutant C229R with bound analog…
2RE8 2.6 Å, Glutaminyl-tRNA synthetase mutant C229R with bound analog…
1EXD 2.7 Å, Crystal structure of a tight-binding glutamine tRNA bound to glutamine aminoacyl tRNA…
1O0B 2.7 Å, Crystal structure of L-glutamine and ampcpp bound to glutamine aminoacyl tRNA synthetase

Browse structure collections

About this viewer

MolViewer shows 1NYL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.