6DK3: Serine hydroxymethyltransferase, mitochondrial

Name: PDB 6DK3: Human mitochondrial serine hydroxymethyltransferase 2
Published: 2018-06-20
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Human mitochondrial serine hydroxymethyltransferase 2. Determined by X-ray diffraction at 2.04 Å resolution. Released 20 Jun 2018.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,389
Mol. weight: 54.11 kDa
Released: 20 Jun 2018

Explore 6DK3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DK3 contains 23 α-helices and 18 β-strands across 1 chain. 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: 23 helices, 18 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
α-helix	111-126	16
β-strand	134-137	4	2
α-helix	143-154	12
β-strand	161-162	2	2
β-strand	164	1	3
β-strand	195	1	3
β-strand	197-198	2	4
β-strand	203-204	2	4
α-helix	206-216	11
β-strand	220-223	4	2
α-helix	234-244	11
β-strand	247-251	5	2
α-helix	253-255	3
α-helix	256-260	5
α-helix	267-269	3
β-strand	273-277	5	2
β-strand	288-293	6	2
β-strand	296-299	4	5
β-strand	306-308	3	5
α-helix	309	1
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	6
α-helix	373-375	3
β-strand	381-385	5	6
α-helix	387-389	3
α-helix	393-402	10
β-strand	405-406	2	1
β-strand	408-410	3	6
β-strand	423-427	5	6
α-helix	429-433	5
α-helix	438-460	23
α-helix	465-474	10
α-helix	476-493	18

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, mitochondrial	A	protein	488	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6DK3_1 Serine hydroxymethyltransferase, mitochondrial (chains A)
GQLVRMAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIAS
ENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGV
NVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYK
LNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHIS
GLVAAKVIPSPFKHADIVTTTTHKTLRGTRSGLIFYRKGVKAVDPKTGREIPYTFEDRIN
FAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGG
TDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQF
REDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAF
PMPGFDEH

Primary citation

HUMAN MITOCHONDRIAL SERINE HYDROXYMETHYLTRANSFERASe 2. Wu, H., Dong, A., Zeng, H. et al. To be published.

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
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)…
8FJT 2.47 Å, Human mitochondrial serine hydroxymethyltransferase (SHMT2) in complex with PLP, glycine…

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