8XND: Serine hydroxymethyltransferase 1

Name: PDB 8XND: Crystal structure of serine hydroxymethyltransferase 1
Published: 2025-04-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of serine hydroxymethyltransferase 1. Determined by X-ray diffraction at 3.45 Å resolution. Released 2 Apr 2025.

Method: X-ray diffraction
Resolution: 3.45 Å
Organism: Homo sapiens
Chains: 4
Atoms: 14,588
Mol. weight: 207.82 kDa
Ligands: PLP
Released: 2 Apr 2025

Explore 8XND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8XND contains 106 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: 27 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	31-46	16
β-strand	48-49	2	1
α-helix	59-66	8
α-helix	68-71	4
β-strand	76-77	2	2
β-strand	80-81	2	2
α-helix	87-103	17
β-strand	111-114	4	3
α-helix	120-131	12
β-strand	137-139	3	3
β-strand	141	1	4
α-helix	143-145	3
α-helix	149-151	3
β-strand	154	1	5
β-strand	159	1	5
α-helix	162-166	5
β-strand	168-169	2	3
β-strand	172	1	4
β-strand	174	1	6
β-strand	181	1	6
α-helix	183-193	11
β-strand	197-201	5	3
α-helix	211-221	11
β-strand	224-228	5	3
α-helix	230-232	3
α-helix	233-237	5
α-helix	244-246	3
β-strand	250-254	5	3
α-helix	257-259	3
β-strand	265-270	6	3
β-strand	273-276	4	7
β-strand	283-285	3	7
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	8
α-helix	350-352	3
β-strand	358-362	5	8
α-helix	363-366	4
α-helix	370-379	10
β-strand	382-383	2	1
β-strand	385-387	3	8
β-strand	400-404	5	8
α-helix	406-409	4
α-helix	415-439	25
α-helix	445-453	9
α-helix	455-473	19

Chain B: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
α-helix	31-46	16
β-strand	48-49	2	9
α-helix	59-65	7
α-helix	68-71	4
β-strand	76-77	2	10
β-strand	80-81	2	10
α-helix	87-103	17
β-strand	111-114	4	11
α-helix	120-131	12
β-strand	137-141	5	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	168-172	5	11
β-strand	174	1	13
β-strand	181	1	13
α-helix	183-193	11
β-strand	197-200	4	11
α-helix	211-221	11
β-strand	224-228	5	11
α-helix	230-232	3
α-helix	233-237	5
α-helix	244-246	3
β-strand	250-254	5	11
α-helix	257-259	3
β-strand	265-270	6	11
β-strand	273-276	4	14
β-strand	283-285	3	14
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	363-366	4
α-helix	370-379	10
β-strand	382-383	2	9
β-strand	385-387	3	15
β-strand	400-404	5	15
α-helix	406-409	4
α-helix	415-439	25
α-helix	445-453	9
α-helix	455-473	19

Chain C: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-21	10
α-helix	31-46	16
β-strand	48-49	2	16
α-helix	59-66	8
α-helix	68-71	4
β-strand	76-77	2	17
β-strand	80-81	2	17
α-helix	87-103	17
β-strand	111-114	4	18
α-helix	120-131	12
β-strand	137-141	5	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	168-172	5	18
β-strand	174	1	20
β-strand	181	1	20
α-helix	183-193	11
β-strand	197-201	5	18
α-helix	211-221	11
β-strand	224-228	5	18
α-helix	230-232	3
α-helix	233-237	5
α-helix	244-246	3
β-strand	250-254	5	18
α-helix	257-259	3
β-strand	265-270	6	18
β-strand	272-275	4	21
β-strand	284-286	3	21
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	22
α-helix	350-352	3
β-strand	358-362	5	22
α-helix	363-366	4
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	406-409	4
α-helix	415-439	25
α-helix	445-453	9
α-helix	455-473	19

Chain D: 26 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-23	12
α-helix	31-46	16
β-strand	48-49	2	23
α-helix	59-65	7
α-helix	68-70	3
β-strand	76-77	2	24
β-strand	80-81	2	24
α-helix	87-103	17
β-strand	111-114	4	25
α-helix	120-131	12
β-strand	137-141	5	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	168-172	5	25
β-strand	174	1	27
β-strand	181	1	27
α-helix	183-193	11
β-strand	197-201	5	25
α-helix	211-221	11
β-strand	224-228	5	25
α-helix	230-232	3
α-helix	233-237	5
α-helix	244-246	3
β-strand	250-254	5	25
α-helix	257-259	3
β-strand	265-270	6	25
β-strand	273-277	5	28
β-strand	282-285	4	28
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
α-helix	350-352	3
β-strand	358-362	5	29
α-helix	363-366	4
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	415-439	25
α-helix	445-453	9
α-helix	455-472	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, cytosolic	A, B, C, D	protein	472	Homo sapiens	P34896 (AlphaFold model)

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

>8XND_1 Serine hydroxymethyltransferase, cytosolic (chains A, B, C, D)
QGDADLWSSHDAMLAQPLKDSDVEVYNIIKKESNRQRVGLELIASENFASRAVLEALGSC
LNNKYSEGYPGQRYYGGTEFIDELETLCQKRALQAYKLDPQCWGVNVQPYSGSPANFAVY
TALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGYINYDQLEE
NARLFHPKLIIAGTSCYSRNLEYARLRKIADENGAYLMADMAHISGLVAAGVVPSPFEHC
HVVTTTTHKTLRGCRAGMIFYRKGVKSVDPATGKEILYNLESLINSAVFPGLQGGPHNHA
IAGVAVALKQAMTLEFKVYQHQVVANCRALSEALTELGYKIVTGGSDNHLILVDLRSKGT
DGGRAEKVLEACSIACNKNTCPGDRSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRG
IELTLQIQSDTGVAATLKEFKERLAGDKYQAAVQALREEVESFASLFPLPGL

Ligands and cofactors

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

Primary citation

Crystal structure of serine hydroxymethyltransferase 1. Fan, S., Wei, X., Lv, R. et al. To be published.

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
8A11 3.52 Å, Cryo-EM structure of the Human SHMT1-RNA complex
6FL5 3.6 Å, Structure of human SHMT1-H135N-R137A-E168N mutant at 3.6 Ang. resolution

Browse structure collections

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