8T4O: Serine hydroxymethyltransferase, mitochondrial

Name: PDB 8T4O: Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF347 inhibitor with no glutamate
Published: 2024-02-21
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine and AGF347 inhibitor with no glutamate. Determined by X-ray diffraction at 2.68 Å resolution. Released 21 Feb 2024.

Method: X-ray diffraction
Resolution: 2.68 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,145
Mol. weight: 110.17 kDa
Ligands: PLG, Y5C
Released: 21 Feb 2024

Explore 8T4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8T4O contains 53 α-helices and 46 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: 26 helices, 25 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	160-162	3	3
β-strand	164	1	4
α-helix	166-168	3
α-helix	172-174	3
β-strand	177	1	5
β-strand	182	1	5
α-helix	185-187	3
β-strand	191-192	2	3
β-strand	195	1	4
β-strand	197	1	6
β-strand	204	1	6
α-helix	206-216	11
β-strand	220-223	4	3
α-helix	234-243	10
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	1	7
β-strand	308	1	7
α-helix	312-317	6
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	371-372	2	8
α-helix	373-375	3
β-strand	381-385	5	8
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	1
β-strand	408-410	3	8
α-helix	411-412	2
β-strand	413	1	9
β-strand	415	1	9
β-strand	423-427	5	8
α-helix	429-432	4
α-helix	438-459	22
α-helix	465-474	10
α-helix	476-494	19

Chain B: 27 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	49-52	4
α-helix	54-69	16
β-strand	71-72	2	10
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	11
β-strand	103-104	2	11
α-helix	110-126	17
β-strand	134-137	4	12
α-helix	143-154	12
β-strand	160-164	5	12
α-helix	166-168	3
α-helix	172-174	3
β-strand	177	1	13
β-strand	182	1	13
α-helix	186-189	4
β-strand	191-195	5	12
β-strand	197	1	14
β-strand	204	1	14
α-helix	206-216	11
β-strand	220-222	3	12
α-helix	234-243	10
β-strand	247-251	5	12
α-helix	256-260	5
α-helix	265-266	2
α-helix	267-269	3
β-strand	273-277	5	12
α-helix	280-282	3
β-strand	288-293	6	12
β-strand	296	1	15
β-strand	308	1	15
α-helix	311-317	7
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-366	22
β-strand	371-372	2	16
α-helix	373-375	3
β-strand	381-385	5	16
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	10
β-strand	408-409	2	16
β-strand	424-427	4	16
α-helix	429-432	4
α-helix	438-459	22
α-helix	465-474	10
α-helix	476-479	4
α-helix	481-494	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, mitochondrial	A, B	protein	493	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8T4O_1 Serine hydroxymethyltransferase, mitochondrial (chains A, B)
MGSSHHHHHHSSGLVPRSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGL
ELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDP
AQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFE
SMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLAD
MAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTF
EDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYS
LVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPAL
TSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQ
FARAFPMPGFDEH

Ligands and cofactors

ID	Name	Formula	Copies
PLG	N-glycine-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-yl-methane]	C10 H15 N2 O7 P	2
Y5C	4-[4-(2-amino-4-oxo-3,4-dihydro-5H-pyrrolo[3,2-d]pyrimidin-5-yl)butyl]-2-fluoro…	C17 H17 F N4 O3	1

Primary citation

Structural Characterization of 5-Substituted Pyrrolo[3,2- d ]pyrimidine Antifolate Inhibitors in Complex with Human Serine Hydroxymethyl Transferase 2. Katinas, J.M., Nayeen, M.J., Schneider, M. et al. Biochemistry (2024). DOI 10.1021/acs.biochem.3c00613 · 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
6M5O 2.3 Å, Co-crystal structure of human serine hydroxymethyltransferase 2 in complex with…
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)…

Browse structure collections

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