6QVL: Human SHMT2

Name: PDB 6QVL: Human SHMT2 in complex with pemetrexed
Published: 2019-09-04
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human SHMT2 in complex with pemetrexed. Determined by X-ray diffraction at 2.28 Å resolution. Released 4 Sept 2019.

Method: X-ray diffraction
Resolution: 2.28 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,641
Mol. weight: 113.48 kDa
Ligands: 4DW, PLP, CA
Released: 4 Sept 2019

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

Secondary structure: helices and β-sheets

6QVL 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	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	253-255	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	6
β-strand	308	1	6
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	438-459	22
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	220-223	4	10
α-helix	234-243	10
α-helix	246	1
β-strand	247-251	5	10
α-helix	253-255	3
α-helix	256-261	6
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	1	13
β-strand	308	1	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
β-strand	381-385	5	14
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	8
β-strand	408-410	3	14
β-strand	423-427	5	14
α-helix	429-433	5
α-helix	438-459	22
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	504	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6QVL_1 Serine hydroxymethyltransferase, mitochondrial (chains A, B)
MLYFSLFWAARPLQRCGQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELL
QREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQ
RRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDV
KRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREV
CDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVD
PKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARA
MADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAIT
PGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQ
RLANLRQRVEQFARAFPMPGFDEH

Ligands and cofactors

ID	Name	Formula	Copies
4DW	N-{4-[2-(2-amino-4-oxo-4,7-dihydro-3H-pyrrolo[2,3-d]pyrimidin-5-yl)ethyl]benzoy…	C20 H19 N5 O6	1
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	2
CA	Calcium ion	Ca	1

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

Primary citation

Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs. Scaletti, E., Jemth, A.S., Helleday, T. et al. FEBS Lett (2019) 593:1863-1873. DOI 10.1002/1873-3468.13455 · 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…
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)…
8FJT 2.47 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…

Browse structure collections

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