1SES: Crystal structures

Crystal structures at 2.5 Å resolution of seryl-tRNA synthetase complexed with two different analogues of seryl-adenylate. Determined by X-ray diffraction at 2.5 Å resolution. Released 31 Jul 1994.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Thermus thermophilus
Chains: 2
Atoms: 6,929
Mol. weight: 96.55 kDa
Ligands: AHX, AMP
Released: 31 Jul 1994

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

Secondary structure: helices and β-sheets

1SES contains 55 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, 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	1
α-helix	114-116	3
α-helix	117	1
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	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	227-232	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	320-323	4
β-strand	329-337	9	1
β-strand	342-353	12	1
α-helix	355-360	6
β-strand	363-365	3	5
β-strand	371-373	3	5
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
α-helix	418-419	2

Chain B: 28 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	4-9	6
α-helix	11-21	11
α-helix	27-57	31
α-helix	58-60	3
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	132-135	4
α-helix	136-143	8
β-strand	146	1	1
α-helix	150-153	4
β-strand	161-162	2	1
α-helix	164-182	19
α-helix	185	1
β-strand	186-189	4	2
β-strand	193-195	3	4
α-helix	196-202	7
α-helix	209-211	3
α-helix	213	1
β-strand	214-215	2	4
β-strand	220-222	3	4
α-helix	226-232	7
β-strand	238-240	3	7
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
α-helix	320-323	4
β-strand	329-337	9	2
α-helix	338-340	3
β-strand	342-351	10	2
α-helix	357-360	4
β-strand	363-365	3	7
β-strand	371-373	3	7
β-strand	375-384	10	2
α-helix	386-395	10
β-strand	396	1	8
β-strand	402-403	2	8
α-helix	406-408	3
α-helix	409-412	4
β-strand	416-417	2	8
α-helix	418-419	2

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

>1SES_1 SERYL-tRNA SYNTHETASE (chains A, B)
MVDLKRLRQEPEVFHRAIREKGVALDLEALLALDREVQELKKRLQEVQTERNQVAKRVPK
APPEEKEALIARGKALGEEAKRLEEALREKEARLEALLLQVPLPPWPGAPVGGEEANREI
KRVGGPPEFSFPPLDHVALMEKNGWWEPRISQVSGSRSYALKGDLALYELALLRFAMDFM
ARRGFLPMTLPSYAREKAFLGTGHFPAYRDQVWAIAETDLYLTGTAEVVLNALHSGEILP
YEALPLRYAGYAPAFRSEAGSFGKDVRGLMRVHQFHKVEQYVLTEASLEASDRAFQELLE
NAEEILRLLELPYRLVEVATGDMGPGKWRQVDIEVYLPSEGRYRETHSCSALLDWQARRA
NLRYRDPEGRVRYAYTLNNTALATPRILAMLLENHQLQDGRVRVPQALIPYMGKEVLEPC
G

Ligands and cofactors

ID	Name	Formula	Copies
AHX	Seryl-hydroxamate-adenosine monophosphate	C13 H20 N7 O9 P	1
AMP	Adenosine monophosphate	C10 H14 N5 O7 P	1

Primary citation

Crystal structures at 2.5 angstrom resolution of seryl-tRNA synthetase complexed with two analogs of seryl adenylate. Belrhali, H., Yaremchuk, A., Tukalo, M. et al. Science (1994) 263:1432-1436. 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
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…
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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