5V7I: Serine hydroxymethyltransferase, mitochondrial

Crystal structure of homo sapiens serine hydroxymethyltransferase 2 (mitochondrial) (SHMT2), in complex with glycine, PLP and folate-competitive pyrazolopyran inhibitor: 6-amino-4-isopropyl-3-methyl-4-(3-(pyrrolidin-1-yl)-5-(trifluoromethyl)phenyl)-1,4-dihydropyrano[2,3-c]pyrazole-5-carbonitrile. Determined by X-ray diffraction at 2.47 Å resolution. Released 11 Oct 2017.

Method: X-ray diffraction
Resolution: 2.47 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,831
Mol. weight: 107.22 kDa
Ligands: GLY, 8Z1
Released: 11 Oct 2017

Explore 5V7I in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V7I contains 53 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: 28 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	172-174	3
β-strand	177	1	4
β-strand	182	1	4
α-helix	185-189	5
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	256-261	6
α-helix	267-269	3
β-strand	273-277	5	3
α-helix	280-282	3
β-strand	288-293	6	3
β-strand	296-299	4	6
α-helix	305	1
β-strand	306-308	3	6
α-helix	309	1
α-helix	312-317	6
α-helix	318-323	6
α-helix	329-341	13
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
α-helix	411-412	2
α-helix	420-421	2
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: 25 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	220-224	5	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	296-300	5	13
β-strand	305-308	4	13
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	14
α-helix	373-375	3
β-strand	381-385	5	14
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	8
β-strand	408-409	2	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	476	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5V7I_1 Serine hydroxymethyltransferase, mitochondrial (chains A, B)
SNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEAL
GSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANL
AVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQ
LALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPF
KHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPH
NHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRP
KGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFI
DEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH

Ligands and cofactors

ID	Name	Formula	Copies
GLY	Glycine	C2 H5 N O2	1
8Z1	(4R)-6-amino-3-methyl-4-(propan-2-yl)-4-[3-(pyrrolidin-1-yl)-5-(trifluoromethyl…	C22 H24 F3 N5 O	2

Water and common crystallization additives (GOL, PEG) are not listed.

Primary citation

Human SHMT inhibitors reveal defective glycine import as a targetable metabolic vulnerability of diffuse large B-cell lymphoma. Ducker, G.S., Ghergurovich, J.M., Mainolfi, N. et al. Proc Natl Acad Sci U S A (2017) 114:11404-11409. DOI 10.1073/pnas.1706617114 · 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…
8FJT 2.47 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…

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