1P7L: S-Adenosylmethionine synthetase

S-Adenosylmethionine synthetase complexed with AMPPNP and Met. Determined by X-ray diffraction at 2.5 Å resolution. Released 2 Mar 2004.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Escherichia coli
Chains: 4
Atoms: 11,960
Mol. weight: 170.44 kDa
Ligands: PPK, SAM, MET, ANP
Released: 2 Mar 2004

Explore 1P7L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1P7L contains 58 α-helices and 66 β-strands across 4 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: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	1
α-helix	15-33	19
β-strand	38-46	9	2
β-strand	49-57	9	2
α-helix	64-75	12
β-strand	78-79	2	3
α-helix	80-82	3
β-strand	84-85	2	3
β-strand	90-96	7	2
α-helix	97-99	3
α-helix	100-106	7
β-strand	120-127	8	4
α-helix	136-153	18
β-strand	160-173	14	1
β-strand	176-189	14	1
α-helix	195-202	8
α-helix	203-207	5
α-helix	213-215	3
β-strand	221-224	4	1
α-helix	234-237	4
β-strand	240-241	2	2
β-strand	265	1	2
α-helix	270-287	18
β-strand	291	1	5
β-strand	293-300	8	4
β-strand	309-313	5	4
β-strand	318	1	5
α-helix	322-332	11
α-helix	337-344	8
α-helix	352-355	4
α-helix	372-378	7

Chain B: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	6
α-helix	15-33	19
β-strand	38-46	9	7
β-strand	49-57	9	7
α-helix	64-75	12
β-strand	78-79	2	8
α-helix	80-82	3
β-strand	84-85	2	8
β-strand	90-96	7	7
α-helix	97-99	3
α-helix	100-106	7
β-strand	120-127	8	9
α-helix	136-153	18
β-strand	160-173	14	6
β-strand	176-189	14	6
α-helix	195-202	8
α-helix	203-207	5
α-helix	213-215	3
β-strand	221-224	4	6
α-helix	234-237	4
β-strand	240-241	2	7
α-helix	246-249	4
β-strand	265	1	7
α-helix	270-287	18
β-strand	291	1	10
β-strand	293-300	8	9
β-strand	309-313	5	9
β-strand	318	1	10
α-helix	322-332	11
α-helix	337-344	8
α-helix	352-354	3
α-helix	372-378	7

Chain C: 14 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	11
α-helix	15-33	19
β-strand	38-46	9	2
β-strand	49-57	9	2
α-helix	64-75	12
β-strand	78-79	2	12
α-helix	80-82	3
β-strand	84-85	2	12
β-strand	90-96	7	2
α-helix	100-106	7
β-strand	116	1	13
β-strand	120-127	8	14
α-helix	136-153	18
β-strand	160-173	14	11
β-strand	176-189	14	11
α-helix	195-202	8
α-helix	203-207	5
α-helix	213-215	3
β-strand	221-224	4	11
α-helix	234-237	4
β-strand	240-241	2	2
β-strand	265	1	2
α-helix	270-287	18
β-strand	291	1	15
β-strand	293-300	8	14
β-strand	302	1	13
β-strand	309-313	5	14
β-strand	318	1	15
α-helix	322-332	11
α-helix	337-344	8
α-helix	352-355	4
α-helix	372-378	7

Chain D: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	3-10	8	16
α-helix	15-33	19
β-strand	38-46	9	7
β-strand	49-57	9	7
α-helix	64-75	12
β-strand	78-79	2	17
α-helix	80-82	3
β-strand	84-85	2	17
β-strand	90-96	7	7
α-helix	100-106	7
β-strand	120-127	8	18
α-helix	136-153	18
β-strand	160-173	14	16
β-strand	176-189	14	16
α-helix	195-202	8
α-helix	203-207	5
β-strand	221-224	4	16
α-helix	234-237	4
β-strand	240-241	2	7
β-strand	265	1	7
α-helix	270-287	18
β-strand	291	1	19
β-strand	293-300	8	18
β-strand	309-313	5	18
β-strand	318	1	19
α-helix	322-332	11
α-helix	337-344	8
α-helix	352-354	3
α-helix	372-378	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
S-adenosylmethionine synthetase	A, B, C, D	protein	383	Escherichia coli	P0A817 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1P7L_1 S-adenosylmethionine synthetase (chains A, B, C, D)
AKHLFTSESVSEGHPDKIADQISDAVLDAILEQDPKARVACETYVKTGMVLVGGEITTSA
WVDIEEITRNTVREIGYVHSDMGFDANSCAVLSAIGKQSPDINQGVDRADPLEQGAGDQG
LMFGYATNETDVLMPAPITYAHRLVQRQAEVRKNGTLPWLRPDAKSQVTFQYDDGKIVGI
DAVVLSTQHSEEIDQKSLQEAVMEEIIKPILPAEWLTSATKFFINPTGRFVIGGPMGDCG
LTGRKIIVDTYGGMARHGGGAFSGKDPSKVDRSAAYAARYVAKNIVAAGLADRCEIQVSY
AIGVAEPTSIMVETFGTEKVPSEQLTLLVREFFDLRPYGLIQMLDLLHPIYKETAAYGHF
GREHFPWEKTDKAQLLRDAAGLK

Ligands and cofactors

ID	Name	Formula	Copies
PPK	(diphosphono)aminophosphonic acid	H6 N O9 P3	2
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2
MET	Methionine	C5 H11 N O2 S	2
ANP	Phosphoaminophosphonic acid-adenylate ester	C10 H17 N6 O12 P3	2
MG	Magnesium ion	Mg	8

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

Primary citation

Crystal structure of the s-adenosylmethionine synthetase ternary complex: a novel catalytic mechanism of s-adenosylmethionine synthesis from ATP and MET. Komoto, J., Yamada, T., Takata, Y. et al. Biochemistry (2004) 43:1821-1831. DOI 10.1021/bi035611t · PubMed

Other PDB entries of the same protein (UniProt P0A817 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7R2W 1.6 Å, Mutant S-adenosylmethionine synthetase from E.coli complexed with AMPPNP and methionine
7LO2 1.89 Å, S-adenosylmethionine synthetase cocrystallized with CTP
7LOO 1.95 Å, S-adenosyl methionine transferase cocrystallized with ATP
7LL3 2.24 Å, S-adenosylmethionine synthetase co-crystallized with UppNHp
7LOZ 2.25 Å, S-adenosylmethionine synthetase
7LOW 2.39 Å, S-adenosylmethionine synthetase
1RG9 2.5 Å, S-Adenosylmethionine synthetase complexed with SAM and PPNP
7LNN 2.5 Å, E. coli S-adenosyl methionine transferase co-crystallized with…
1MXA 2.8 Å, S-adenosylmethionine synthetase with ppi
1MXB 2.8 Å, S-adenosylmethionine synthetase with ADP
8BB1 2.8 Å, T3 SAM lyase in complex with S-adenosylmethionine synthase
1MXC 3.0 Å, S-adenosylmethionine synthetase with 8-br-ADP

Browse structure collections

About this viewer

MolViewer shows 1P7L 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.