1SRY: Seryl-tRNA synthetase from thermus thermophilus

Refined crystal structure of the seryl-tRNA synthetase from thermus thermophilus at 2.5 Å resolution. Determined by X-ray diffraction at 2.5 Å resolution. Released 31 Jan 1994.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Thermus thermophilus
Chains: 2
Atoms: 6,936
Mol. weight: 95.76 kDa
Released: 31 Jan 1994

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

Secondary structure: helices and β-sheets

1SRY contains 50 α-helices and 42 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: 25 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-20	10
α-helix	27-57	31
α-helix	63-65	3
α-helix	67-98	32
α-helix	101-106	6
α-helix	110-111	2
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	209-211	3
β-strand	214	1	3
β-strand	215	1	4
β-strand	220-222	3	3
α-helix	227-232	6
β-strand	238-240	3	5
α-helix	241-243	3
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
β-strand	329-337	9	1
β-strand	342-353	12	1
α-helix	357-360	4
β-strand	363-365	3	5
β-strand	371-373	3	5
α-helix	374	1
β-strand	375-384	10	1
α-helix	386-395	10
β-strand	396	1	6
β-strand	402-403	2	6
α-helix	404-405	2
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	6

Chain B: 25 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-20	10
α-helix	27-56	30
β-strand	59	1	7
β-strand	61	1	7
α-helix	63-98	36
α-helix	101-106	6
α-helix	110	1
α-helix	114-116	3
β-strand	118-123	6	2
α-helix	132-134	3
α-helix	136-143	8
β-strand	146	1	1
α-helix	150-153	4
β-strand	161-162	2	1
α-helix	163-181	19
β-strand	186-189	4	2
β-strand	193-195	3	8
α-helix	196-202	7
α-helix	209-211	3
α-helix	213	1
β-strand	214	1	8
β-strand	215	1	4
β-strand	220-222	3	8
α-helix	227-232	6
β-strand	238-240	3	9
α-helix	241-243	3
α-helix	244	1
β-strand	246-255	10	2
β-strand	274-284	11	2
α-helix	288-309	22
β-strand	313-317	5	2
α-helix	318-319	2
β-strand	329-337	9	2
α-helix	338-340	3
β-strand	342-353	12	2
α-helix	357-360	4
β-strand	363-365	3	9
β-strand	371-373	3	9
β-strand	375-384	10	2
α-helix	386-395	10
β-strand	396	1	10
β-strand	402-403	2	10
α-helix	404-405	2
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Seryl-tRNA synthetase	A, B	protein	421	Thermus thermophilus	P34945 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>1SRY_1 SERYL-tRNA SYNTHETASE (chains A, B)
MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPK
APPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREI
KRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFM
ARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILP
YEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLE
NAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRA
NLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPC
G

Primary citation

Refined crystal structure of the seryl-tRNA synthetase from Thermus thermophilus at 2.5 A resolution. Fujinaga, M., Berthet-Colominas, C., Yaremchuk, A.D. et al. J Mol Biol (1993) 234:222-233. DOI 10.1006/jmbi.1993.1576 · 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…
1SET 2.55 Å, Crystal structures at 2.5 Å resolution of seryl-tRNA synthetase complexed with two…
9QRP 2.7 Å, Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate…
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

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