6M5O: Serine hydroxymethyltransferase, mitochondrial

Name: PDB 6M5O: Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid
Published: 2021-01-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with Pyridoxal 5'-phosphate (PLP) and glycodeoxycholic acid. Determined by X-ray diffraction at 2.3 Å resolution. Released 20 Jan 2021.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,794
Mol. weight: 113.62 kDa
Ligands: DXC, GLY
Released: 20 Jan 2021

Explore 6M5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6M5O contains 49 α-helices and 42 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: 25 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	1
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	2
β-strand	103-104	2	2
α-helix	110-126	17
β-strand	134-137	4	3
α-helix	143-154	12
β-strand	160-164	5	3
α-helix	166-168	3
α-helix	172-174	3
β-strand	177	1	4
β-strand	182	1	4
α-helix	186-189	4
β-strand	191-195	5	3
β-strand	197-198	2	5
β-strand	203-204	2	5
α-helix	206-216	11
β-strand	220-223	4	3
α-helix	234-244	11
β-strand	247-251	5	3
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	3
α-helix	280-282	3
β-strand	288-293	6	3
β-strand	296-298	3	6
β-strand	307-308	2	6
α-helix	312-317	6
α-helix	318-323	6
α-helix	329-343	15
α-helix	345-367	23
β-strand	371-372	2	7
α-helix	373-375	3
β-strand	381-385	5	7
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	1
β-strand	408-410	3	7
β-strand	423-427	5	7
α-helix	429-433	5
α-helix	438-460	23
α-helix	465-474	10
α-helix	476-494	19

Chain B: 24 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	8
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	9
β-strand	103-104	2	9
α-helix	110-126	17
β-strand	134-137	4	10
α-helix	143-154	12
β-strand	160-164	5	10
α-helix	172-174	3
β-strand	177	1	11
β-strand	182	1	11
α-helix	185-189	5
β-strand	191-195	5	10
β-strand	197	1	12
β-strand	204	1	12
α-helix	206-216	11
β-strand	220-223	4	10
α-helix	234-243	10
β-strand	247-251	5	10
α-helix	253-255	3
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	10
α-helix	280-282	3
β-strand	288-293	6	10
β-strand	296-298	3	13
β-strand	307-308	2	13
α-helix	311-317	7
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	371-372	2	14
α-helix	373-375	3
β-strand	381-385	5	14
α-helix	393-402	10
β-strand	405-406	2	8
β-strand	408-410	3	14
β-strand	423-427	5	14
α-helix	429-433	5
α-helix	438-460	23
α-helix	465-474	10
α-helix	476-494	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, mitochondrial	A, B	protein	507	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6M5O_1 Serine hydroxymethyltransferase, mitochondrial (chains A, B)
MGSSHHHHHHSSGLVPRGSGQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMW
ELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIEL
LCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYM
SDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARM
REVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVK
AVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKN
ARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRS
AITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSE
TSQRLANLRQRVEQFARAFPMPGFDEH

Ligands and cofactors

ID	Name	Formula	Copies
DXC	(3ALPHA,5BETA,12ALPHA)-3,12-dihydroxycholan-24-oic acid	C24 H40 O4	2
GLY	Glycine	C2 H5 N O2	2

Primary citation

Structural basis for selective inhibition of human serine hydroxymethyltransferase by secondary bile acid conjugate. Ota, T., Senoo, A., Shirakawa, M. et al. iScience (2021) 24:102036-102036. DOI 10.1016/j.isci.2021.102036 · PubMed

Other PDB entries of the same protein (UniProt P34897 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8AQL 1.23 Å, High-resolution crystal structure of human SHMT2
29LK 1.26 Å, High-resolution structure of human SHMT2 in complex with PLP-Ser (external aldimine)
9RWD 1.3 Å, High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)
32JY 1.8 Å, Structure of the pathogenic variant G423S of Human SHMT2
6DK3 2.04 Å, Human mitochondrial serine hydroxymethyltransferase 2
9BOX 2.1 Å, Room-temperature X-ray structure of human mitochondrial serine hydroxymethyltransferase…
32JA 2.2 Å, Structure of the pathogenic variant T186R of Human SHMT2 in the apo open dimeric…
6QVL 2.28 Å, Human SHMT2 in complex with pemetrexed
6QVG 2.32 Å, Human SHMT2 in complex with lometrexol
8GKW 2.38 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…
5V7I 2.47 Å, Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial)…
8FJT 2.47 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…

Browse structure collections

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