4GND: NSD3 tandem PHD5-C5HCH domains

Name: PDB 4GND: Crystal Structure of NSD3 tandem PHD5-C5HCH domains
Published: 2013-01-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal Structure of NSD3 tandem PHD5-C5HCH domains. Determined by X-ray diffraction at 2.27 Å resolution. Released 2 Jan 2013.

Method: X-ray diffraction
Resolution: 2.27 Å
Organism: Homo sapiens
Chains: 2
Atoms: 1,629
Mol. weight: 24.64 kDa
Ligands: ZN
Released: 2 Jan 2013

Explore 4GND in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4GND contains 9 α-helices and 19 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: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	1334-1335	2	1
α-helix	1336	1
β-strand	1344-1345	2	1
α-helix	1348-1350	3
α-helix	1363-1365	3
β-strand	1366	1	2
β-strand	1373	1	2
α-helix	1374	1
β-strand	1376-1377	2	3
β-strand	1384-1385	2	3
α-helix	1387-1389	3
β-strand	1395-1396	2	4
β-strand	1403-1404	2	4

Chain C: 4 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	1323	1	5
β-strand	1324	1	6
β-strand	1330	1	5
β-strand	1334-1335	2	6
β-strand	1344-1345	2	6
α-helix	1347-1350	4
α-helix	1355-1357	3
α-helix	1363-1365	3
β-strand	1366	1	7
β-strand	1373	1	7
α-helix	1374	1
β-strand	1376-1377	2	8
β-strand	1384-1385	2	8
β-strand	1395-1396	2	9
β-strand	1403-1404	2	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase NSD3	A, C	protein	107	Homo sapiens	Q9BZ95 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4GND_1 Histone-lysine N-methyltransferase NSD3 (chains A, C)
SNARKIKTEPKQMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQ
CDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	8

Primary citation

The methyltransferase NSD3 has chromatin-binding motifs, PHD5-C5HCH, that are distinct from other NSD (nuclear receptor SET domain) family members in their histone H3 recognition. He, C., Li, F., Zhang, J. et al. J Biol Chem (2013) 288:4692-4703. DOI 10.1074/jbc.M112.426148 · PubMed

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
5UPD 1.8 Å, Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1…
6G2O 1.81 Å, X-ray structure of NSD3-PWWP1 in complex with compound BI-9321

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