5UPD: Histone-lysine N-methyltransferase NSD3

Name: PDB 5UPD: Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)
Published: 2017-02-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1). Determined by X-ray diffraction at 1.8 Å resolution. Released 15 Feb 2017.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,892
Mol. weight: 27.09 kDa
Ligands: SAM, ZN
Released: 15 Feb 2017

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

Secondary structure: helices and β-sheets

5UPD contains 9 α-helices and 19 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: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	1074-1075	2	1
β-strand	1080-1081	2	2
α-helix	1092-1094	3
α-helix	1115-1118	4
β-strand	1121	1	3
α-helix	1122-1124	3
α-helix	1138-1141	4
β-strand	1147-1151	5	4
β-strand	1157-1161	5	4
β-strand	1165	1	5
β-strand	1170-1174	5	3
β-strand	1177-1179	3	2
α-helix	1181-1193	13
β-strand	1201-1205	5	2
β-strand	1208-1211	4	2
β-strand	1215-1216	2	1
α-helix	1218-1221	4
α-helix	1222	1
β-strand	1223-1224	2	3
β-strand	1230-1237	8	3
β-strand	1240-1247	8	3
β-strand	1251	1	5
α-helix	1255	1
β-strand	1256	1	4
α-helix	1257	1
β-strand	1258-1259	2	3
β-strand	1272	1	6
β-strand	1283	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD3	A	protein	233	Homo sapiens	Q9BZ95 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5UPD_1 Histone-lysine N-methyltransferase NSD3 (chains A)
GQRESKEALEIEKNSRKPPPYKHIKANKVIGKVQIQVADLSEIPRCNCKPADENPCGLES
ECLNRMLQYECHPQVCPAGDRCQNQCFTKRLYPDAEIIKTERRGWGLRTKRSIKKGEFVN
EYVGELIDEEECRLRIKRAHENSVTNFYMLTVTKDRIIDAGPKGNYSRFMNHSCNPNCET
QKWTVNGDVRVGLFALCDIPAGMELTFNYNLDCLGNGRTECHCGADNCSGFLG

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	3

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

Primary citation

Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1). Tempel, W., Yu, W., Dong, A. et al. To be published.

Other PDB entries of the same protein (UniProt Q9BZ95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6G25 1.43 Å, X-ray structure of NSD3-PWWP1 in complex with compound 4
4GNE 1.47 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7
4GNF 1.55 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15
6CEN 1.61 Å, Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21
6G2B 1.61 Å, X-ray structure of NSD3-PWWP1 in complex with compound 8
6G27 1.65 Å, X-ray structure of NSD3-PWWP1 in complex with compound 5
6G29 1.7 Å, X-ray structure of NSD3-PWWP1 in complex with compound 6
4GNG 1.73 Å, Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide
6G2F 1.74 Å, X-ray structure of NSD3-PWWP1 in complex with compound 16
6G2C 1.76 Å, X-ray structure of NSD3-PWWP1 in complex with compound 9
6G2O 1.81 Å, X-ray structure of NSD3-PWWP1 in complex with compound BI-9321
6G2E 1.85 Å, X-ray structure of NSD3-PWWP1 in complex with compound 13

Browse structure collections

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