1SER: Protein)

The 2.9 Å crystal structure of T. Thermophilus seryl-tRNA synthetase complexed with tRNA ser. Determined by X-ray diffraction at 2.9 Å resolution. Released 30 Apr 1994.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Thermus thermophilus
Chains: 3
Atoms: 7,780
Mol. weight: 126.14 kDa
Released: 30 Apr 1994

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

Secondary structure: helices and β-sheets

1SER contains 50 α-helices and 40 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: 26 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-21	11
α-helix	27-36	10
α-helix	90-98	9
α-helix	101-106	6
α-helix	110-111	2
α-helix	114-116	3
β-strand	118-123	6	1
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	164-182	19
α-helix	185	1
β-strand	186-189	4	1
β-strand	193-195	3	3
α-helix	196-202	7
α-helix	209-211	3
α-helix	213	1
β-strand	214	1	3
β-strand	215	1	4
β-strand	220-222	3	3
α-helix	227-233	7
β-strand	238-240	3	5
α-helix	241-243	3
α-helix	244	1
β-strand	246-255	10	1
β-strand	274-284	11	1
α-helix	288-309	22
β-strand	313-317	5	1
α-helix	318-319	2
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	5
β-strand	371-373	3	5
β-strand	375-384	10	1
α-helix	386-394	9
β-strand	396	1	6
β-strand	402-403	2	6
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	6
α-helix	418-419	2

Chain B: 24 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	504-509	6
α-helix	511-520	10
α-helix	527-557	31
α-helix	565-598	34
α-helix	601-606	6
α-helix	610-611	2
α-helix	614-616	3
β-strand	618-623	6	2
α-helix	632-635	4
α-helix	636-642	7
β-strand	646	1	1
α-helix	650-654	5
β-strand	661-662	2	1
α-helix	664-682	19
β-strand	686-689	4	2
β-strand	693-695	3	7
α-helix	696-702	7
α-helix	709-711	3
β-strand	714	1	7
β-strand	715	1	4
β-strand	720-722	3	7
α-helix	727-732	6
β-strand	738-740	3	8
α-helix	741-743	3
β-strand	746-755	10	2
β-strand	774-784	11	2
α-helix	788-808	21
β-strand	813-817	5	2
α-helix	818-819	2
α-helix	820-823	4
β-strand	829-837	9	2
α-helix	838-840	3
β-strand	842-851	10	2
α-helix	857-860	4
β-strand	863-865	3	8
β-strand	871-873	3	8
β-strand	875-884	10	2
α-helix	886-894	9
β-strand	896	1	9
β-strand	902-903	2	9
α-helix	906-908	3
α-helix	909-912	4
β-strand	916-917	2	9
α-helix	918-919	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Trnaser	T	RNA	94	Thermus thermophilus
Protein (seryl-tRNA synthetase (E.C.6.1.1.11))	A, B	protein	421	Thermus thermophilus	P34945 (AlphaFold model)

Sequence of entity 1 (T), FASTA

>1SER_1 TRNASER (chains T)
GGAGAGGUGCCCGAGUGGCUGAAGGGACACGACUGGAAAUCGUGUAGGGGGGCUUAAACC
UCCCUCGCGGGUUCGAAUCCCGCCCUCUCCGCCA

Sequence of entity 2 (A, B), FASTA

>1SER_2 PROTEIN (SERYL-TRNA SYNTHETASE (E.C.6.1.1.11)) (chains A, B)
MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPK
APPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREI
KRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFM
ARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILP
YEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLE
NAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRA
NLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPC
G

Primary citation

The 2.9 A crystal structure of T. thermophilus seryl-tRNA synthetase complexed with tRNA(Ser). Biou, V., Yaremchuk, A., Tukalo, M. et al. Science (1994) 263:1404-1410. 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…
9QRP 2.7 Å, Thermus thermophilus seryl-tRNA synthetase bound to tRNA(ser)(GGA) and seryl-adenylate…
5IEA 3.26 Å, TRIM5 B-box2 and coiled-coil chimera

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