7BYI: SHMT2

Structure of SHMT2 in complex with CBX. Determined by X-ray diffraction at 2.76 Å resolution. Released 15 Sept 2021.

Method: X-ray diffraction
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 2
Atoms: 7,363
Mol. weight: 108.14 kDa
Ligands: PO4, CBO
Released: 15 Sept 2021

Explore 7BYI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7BYI contains 48 α-helices and 41 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: 23 helices, 20 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	110-126	17
β-strand	134-137	4	2
α-helix	143-154	12
β-strand	160-163	4	2
α-helix	172-174	3
β-strand	177	1	3
β-strand	182	1	3
α-helix	186-189	4
β-strand	191-194	4	2
β-strand	197-198	2	4
β-strand	203-204	2	4
α-helix	206-215	10
β-strand	220-223	4	2
α-helix	237-244	8
β-strand	247-251	5	2
α-helix	256-261	6
α-helix	267-269	3
β-strand	273-277	5	2
β-strand	288-293	6	2
β-strand	296-298	3	5
α-helix	306	1
β-strand	307-308	2	5
α-helix	309	1
α-helix	311-317	7
α-helix	318-323	6
α-helix	329-342	14
α-helix	345-367	23
β-strand	372	1	6
β-strand	375	1	6
β-strand	381-385	5	6
α-helix	393-401	9
β-strand	405-406	2	1
β-strand	408-410	3	6
β-strand	423-427	5	6
α-helix	429-432	4
α-helix	438-459	22
α-helix	466-474	9
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	7
α-helix	82-88	7
α-helix	91-94	4
β-strand	99-100	2	8
β-strand	103-104	2	8
α-helix	110-127	18
β-strand	134-137	4	9
α-helix	143-154	12
β-strand	160-163	4	9
α-helix	172-174	3
β-strand	177	1	10
β-strand	182	1	10
α-helix	186-189	4
β-strand	191-192	2	9
β-strand	197	1	11
β-strand	204	1	11
α-helix	206-215	10
β-strand	220-224	5	9
α-helix	234-244	11
α-helix	246	1
β-strand	247-251	5	9
α-helix	256-261	6
α-helix	265-266	2
α-helix	267-269	3
β-strand	273-277	5	9
α-helix	280-282	3
β-strand	288-293	6	9
β-strand	296	1	12
β-strand	308	1	12
α-helix	311-317	7
α-helix	318-323	6
α-helix	329-340	12
α-helix	345-364	20
α-helix	365-369	5
β-strand	371-373	3	13
β-strand	381-385	5	13
α-helix	393-401	9
β-strand	405-406	2	7
β-strand	408-410	3	13
β-strand	423-427	5	13
α-helix	429-432	4
α-helix	440-459	20
α-helix	465-474	10
α-helix	476-494	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine hydroxymethyltransferase, mitochondrial	A	protein	483	Homo sapiens	P34897 (AlphaFold model)
Serine hydroxymethyltransferase, mitochondrial	B	protein	483	Homo sapiens	P34897 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7BYI_1 Serine hydroxymethyltransferase, mitochondrial (chains A)
MAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCS
RAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPY
SGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKT
GLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAG
KVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFP
SLQGGPHNHAIAAVAVALKQAATPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHL
VLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDF
RRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH

Sequence of entity 2 (B), FASTA

>7BYI_2 Serine hydroxymethyltransferase, mitochondrial (chains B)
MAIRAQHSNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCS
RAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPY
SGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYGLAPKT
GLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAA
KVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREAPYTFEDRINFAVFP
SLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGGYLVSGGTDNHL
VLVDLRPKGGGGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDF
RRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGF
DEH

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
CBO	Carbenoxolone	C34 H50 O7	2

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

Primary citation

Structure of SHMT2 with CBX. Li, L., Su, D. 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
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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