9QRP: Thermus thermophilus seryl-tRNA synthetase

Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate analogue. Determined by X-ray diffraction at 2.7 Å resolution. Released 14 May 2025.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Thermus thermophilus HB8
Chains: 3
Atoms: 8,846
Mol. weight: 128.04 kDa
Ligands: MN, SSA
Released: 14 May 2025

Explore 9QRP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9QRP contains 51 α-helices and 39 β-strands across 2 chains. 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: 27 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-21	11
α-helix	27-49	23
α-helix	79-98	20
α-helix	101-106	6
α-helix	110	1
α-helix	114-116	3
β-strand	118-123	6	1
α-helix	125-127	3
α-helix	132-135	4
α-helix	136-143	8
β-strand	146	1	2
α-helix	150-154	5
β-strand	161-162	2	2
α-helix	163-182	20
β-strand	186-189	4	1
β-strand	193-195	3	3
α-helix	196-202	7
α-helix	204-207	4
α-helix	209-211	3
β-strand	214-215	2	3
β-strand	220-222	3	3
α-helix	227-232	6
β-strand	238-240	3	4
α-helix	241-243	3
α-helix	244	1
β-strand	246-255	10	1
β-strand	274-284	11	1
α-helix	288-308	21
β-strand	313-317	5	1
α-helix	318-319	2
α-helix	320-322	3
β-strand	329-337	9	1
α-helix	338-340	3
β-strand	342-351	10	1
α-helix	357-360	4
β-strand	363-365	3	4
β-strand	371-373	3	4
β-strand	375-384	10	1
α-helix	386-394	9
β-strand	396	1	5
β-strand	402-403	2	5
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	5
α-helix	418-419	2

Chain B: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-21	11
α-helix	27-57	31
α-helix	63-98	36
α-helix	101-106	6
α-helix	110-111	2
α-helix	114-116	3
β-strand	118-123	6	2
α-helix	136-143	8
β-strand	146	1	1
α-helix	150-154	5
β-strand	161-162	2	1
α-helix	163-181	19
β-strand	186-189	4	2
β-strand	193-195	3	3
α-helix	196-202	7
α-helix	209-211	3
β-strand	213-215	3	3
β-strand	220-222	3	3
α-helix	227-232	6
β-strand	237-240	4	6
α-helix	241-243	3
α-helix	244	1
β-strand	246-255	10	2
β-strand	274-284	11	2
α-helix	288-308	21
β-strand	313-317	5	2
α-helix	318-319	2
α-helix	320-323	4
β-strand	329-337	9	2
α-helix	338-340	3
β-strand	342-351	10	2
α-helix	355-360	6
β-strand	362-365	4	6
β-strand	371-373	3	6
β-strand	375-384	10	2
α-helix	386-394	9
β-strand	396	1	7
β-strand	402	1	7
β-strand	403	1	8
α-helix	406-408	3
α-helix	409-412	4
β-strand	416	1	8
α-helix	417-419	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine--tRNA ligase	A, B	protein	421	Thermus thermophilus HB8	P34945 (AlphaFold model)
tRNA(Ser), GGA anticodon	T	RNA	94	Thermus thermophilus HB8

Sequence of entity 1 (A, B), FASTA

>9QRP_1 Serine--tRNA ligase (chains A, B)
MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPK
APPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREI
KRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFM
ARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILP
YEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLE
NAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRA
NLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPC
G

Sequence of entity 2 (T), FASTA

>9QRP_2 tRNA(Ser), GGA anticodon (chains T)
GGAGAGGUGCCCGAGUGGCUGAAGGGACACGACUGGAAAUCGUGUAGGGGGGCUUAAACC
UCCCUCGCGGGUUCGAAUCCCGCCCUCUCCGCCA

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	1
SSA	5'-O-(N-(L-seryl)-sulfamoyl)adenosine	C13 H19 N7 O8 S	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

The crystal structure of the ternary complex of T.thermophilus seryl-tRNA synthetase with tRNA(Ser) and a seryl-adenylate analogue reveals a conformational switch in the active site. Cusack, S., Yaremchuk, A., Tukalo, M. EMBO J (1996) 15:2834-2842. PubMed

Other PDB entries of the same protein (UniProt P34945 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EIU 1.91 Å, Mini TRIM5 B-box 2 dimer C2 crystal form
5F7T 2.29 Å, TRIM5 B-box2 and coiled-coil chimera
5VA4 2.31 Å, TRIM-Cyclophilin A B-box 2 and coiled-coil chimera
1SES 2.5 Å, Crystal structures at 2.5 Å resolution of seryl-tRNA synthetase complexed with two…
1SRY 2.5 Å, Refined crystal structure of the seryl-tRNA synthetase from thermus thermophilus at 2.5…
1SET 2.55 Å, Crystal structures at 2.5 Å resolution of seryl-tRNA synthetase complexed with two…
1SER 2.9 Å, The 2.9 Å crystal structure of T. Thermophilus seryl-tRNA synthetase complexed with tRNA…
5IEA 3.26 Å, TRIM5 B-box2 and coiled-coil chimera

Browse structure collections

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