6FL5: Serine hydroxymethyltransferase, cytosolic

Name: PDB 6FL5: Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution
Published: 2018-10-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution. Determined by X-ray diffraction at 3.6 Å resolution. Released 10 Oct 2018.

Method: X-ray diffraction
Resolution: 3.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,389
Mol. weight: 207.91 kDa
Ligands: PLP
Released: 10 Oct 2018

Explore 6FL5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6FL5 contains 113 α-helices and 86 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: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	13-22	10
α-helix	26-29	4
α-helix	31-46	16
β-strand	48-49	2	1
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111-114	4	2
α-helix	120-131	12
β-strand	137-139	3	2
β-strand	141	1	3
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	4
β-strand	159	1	4
α-helix	162-166	5
β-strand	168-169	2	2
β-strand	172	1	3
β-strand	174	1	5
β-strand	181	1	5
α-helix	183-193	11
β-strand	197-201	5	2
α-helix	211-220	10
β-strand	224-228	5	2
α-helix	233-238	6
β-strand	250-254	5	2
α-helix	257-259	3
β-strand	265-270	6	2
β-strand	273-276	4	6
α-helix	282	1
β-strand	283-285	3	6
α-helix	286	1
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	348-349	2	7
α-helix	350-352	3
β-strand	358-362	5	7
α-helix	363-365	3
α-helix	370-379	10
β-strand	382-383	2	1
β-strand	385-387	3	7
α-helix	388-389	2
β-strand	400-404	5	7
α-helix	406-411	6
α-helix	415-438	24
α-helix	445-453	9
α-helix	458-473	16

Chain D: 28 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
α-helix	26-29	4
α-helix	31-45	15
β-strand	48-49	2	8
α-helix	59-65	7
α-helix	68-70	3
β-strand	76-77	2	9
β-strand	80-81	2	9
α-helix	87-103	17
β-strand	111-114	4	10
α-helix	120-127	8
α-helix	128-132	5
β-strand	137-139	3	10
β-strand	141	1	11
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	12
β-strand	159	1	12
α-helix	162-166	5
β-strand	168-169	2	10
β-strand	172	1	11
β-strand	174	1	13
β-strand	181	1	13
α-helix	183-193	11
β-strand	197-201	5	10
α-helix	211-221	11
β-strand	224-228	5	10
α-helix	233-238	6
β-strand	250-254	5	10
α-helix	257-259	3
β-strand	265-270	6	10
β-strand	273-276	4	14
α-helix	282	1
β-strand	283-285	3	14
α-helix	286	1
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	348-349	2	15
α-helix	350-352	3
β-strand	358-362	5	15
α-helix	363-365	3
α-helix	370-378	9
β-strand	382-383	2	8
β-strand	385-387	3	15
β-strand	400-404	5	15
α-helix	406-411	6
α-helix	415-438	24
α-helix	445-453	9
α-helix	458-472	15

Chain G: 28 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	13-23	11
α-helix	26-29	4
α-helix	31-46	16
β-strand	48-49	2	16
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111-114	4	17
α-helix	120-127	8
α-helix	128-132	5
β-strand	138-139	2	17
β-strand	141	1	18
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	19
β-strand	159	1	19
α-helix	162-166	5
β-strand	169	1	17
β-strand	172	1	18
β-strand	174	1	20
β-strand	181	1	20
α-helix	183-193	11
β-strand	197-201	5	17
α-helix	211-220	10
β-strand	224-228	5	17
α-helix	233-238	6
β-strand	250-254	5	17
α-helix	257-259	3
β-strand	265-270	6	17
β-strand	273-276	4	21
β-strand	283-285	3	21
α-helix	286	1
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-318	13
α-helix	322-343	22
β-strand	348-349	2	22
α-helix	350-352	3
β-strand	358-362	5	22
α-helix	363-365	3
α-helix	370-379	10
β-strand	382-383	2	16
β-strand	385-387	3	22
α-helix	388-389	2
β-strand	400-404	5	22
α-helix	406-411	6
α-helix	415-438	24
α-helix	445-452	8
α-helix	457-472	16

Chain J: 29 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	17-22	6
α-helix	26-29	4
α-helix	31-46	16
β-strand	48-49	2	23
α-helix	59-65	7
α-helix	68-70	3
α-helix	87-103	17
β-strand	111-114	4	24
α-helix	120-127	8
α-helix	128-132	5
β-strand	137-139	3	24
β-strand	141	1	25
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	26
β-strand	159	1	26
α-helix	162-166	5
β-strand	168-169	2	24
β-strand	172	1	25
β-strand	174	1	27
β-strand	181	1	27
α-helix	183-193	11
β-strand	197-201	5	24
α-helix	211-221	11
β-strand	224-228	5	24
α-helix	230-232	3
α-helix	233-238	6
α-helix	244-246	3
β-strand	250-254	5	24
α-helix	257-259	3
β-strand	265-270	6	24
β-strand	273-276	4	28
α-helix	282	1
β-strand	283-285	3	28
α-helix	286	1
α-helix	288-294	7
α-helix	295-300	6
α-helix	306-319	14
α-helix	322-344	23
β-strand	348-349	2	29
β-strand	358-362	5	29
α-helix	363-365	3
α-helix	370-379	10
β-strand	382-383	2	23
β-strand	385-387	3	29
β-strand	400-404	5	29
α-helix	406-409	4
α-helix	415-436	22
α-helix	446-453	8
α-helix	458-472	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, cytosolic	A, D, G, J	protein	471	Homo sapiens	P34896 (AlphaFold model)

Sequence of entity 1 (A, D, G, J), FASTA

>6FL5_1 Serine hydroxymethyltransferase, cytosolic (chains A, D, G, J)
DADLWSSHDKMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFASRAVLEALGSCLN
NKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQPYSGSPANFAVYTA
LVEPNGAIMGLDLPDGGHLTHGFMTDKKKISATSIFFNSMPYKVNPDTGYINYDQLEENA
RLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVAAGVVPSPFEHCHV
VTTTTHKTLRGCRAGMIFYRKGVKSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIA
GVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNHLILVDLRSKGTDG
GRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIE
LTLQIQSDTGVRATLKEFKERLAGDKYQAAVQALREEVESFASLFPLPGLP

Ligands and cofactors

ID	Name	Formula	Copies
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	4

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

Primary citation

The catalytic activity of serine hydroxymethyltransferase is essential for de novo nuclear dTMP synthesis in lung cancer cells. Giardina, G., Paone, A., Tramonti, A. et al. FEBS J (2018) 285:3238-3253. DOI 10.1111/febs.14610 · PubMed

Other PDB entries of the same protein (UniProt P34896 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7RJP 1.25 Å, Crystal structure of human Bromodomain containing protein 4 (BRD4) in complex with SHMT
7RJL 1.5 Å, Crystal structure of human Bromodomain containing protein 3 (BRD3) in complex with SHMT
1BJ4 2.65 Å, Recombinant serine hydroxymethyltransferase (HUMAN)
6M5W 3.1 Å, Co-crystal structure of human serine hydroxymethyltransferase 1 in complex with…
8R7H 3.29 Å, Cryo-EM structure of Human SHMT1
8XND 3.45 Å, Crystal structure of serine hydroxymethyltransferase 1
8A11 3.52 Å, Cryo-EM structure of the Human SHMT1-RNA complex

Browse structure collections

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