4gnd

Crystal Structure of NSD3 tandem PHD5-C5HCH domains

Method: X-RAY DIFFRACTION D_max: 91.9 Å Quality: REASONABLE

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Histone-lysine N-methyltransferase NSD3

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1310–1413	Fragment：UNP RESIDUES 1310-1413	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Hepes, 1.1M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.27 Å R-free 0.219
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1310–1413	Fragment：UNP RESIDUES 1310-1413	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Hepes, 1.1M Sodium Malonate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 2.27 Å R-free 0.219

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 4GND	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DAQ Solution structure of second PWWP domain of WHSC1L1 protein Deposited 2005-12-14	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 957–1053（97 aa） Fragment：PWWP domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120；Pressure ambient NMR sample composition 0.60mM PWWP domain; U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2NCZ Solution NMR structures of BRD4 ET domain in complex with NSD3_1 peptide Deposited 2016-04-18	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 152–163（12 aa） Fragment：residues 152-163	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O \| 100% D2O NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2ND1 Solution NMR structures of BRD4 ET domain in complex with NSD3_3 peptide Deposited 2016-04-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 593–605（13 aa） Fragment：residues 593-605	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 100% D2O \| 100% D2O NMR sample composition 10 mM sodium phosphate, 100 mM sodium chloride, 2 mM [U-100% 2H] DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
4GNE Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7 Deposited 2012-08-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Tris-HCl pH 7.0, 30% (w/v) PEG 3000, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 1.47 Å R-free 0.178
4GNF Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15 Deposited 2012-08-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 1.55 Å R-free 0.205
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 1.73 Å R-free 0.214
4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1310–1413（104 aa） Fragment：UNP RESIDUES 1310-1413	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K	Resolution 1.73 Å R-free 0.214
4RXJ crystal structure of WHSC1L1-PWWP2 Deposited 2014-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 953–1064（112 aa）	Not recorded	UNX UNKNOWN LIGAND × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 3.5；293 K；25% w/v PEG3350, 10% citric acid, pH 3.5, vapor diffusion, temperature 293K, VAPOR DIFFUSION	Resolution 2.10 Å R-free 0.272
5UPD Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1) Deposited 2017-02-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1054–1285（232 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 UNX UNKNOWN LIGAND × 17 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；20% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine	Resolution 1.80 Å R-free 0.218
6CEN Crystal Structure of WHSC1L1 in Complex with Inhibitor PEP21 Deposited 2018-02-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1058–1285（228 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；291 K；0.1 M Bis-Tris pH 6.5, 20% w/v PEG5000MME	Resolution 1.61 Å R-free 0.215
6G24 X-ray structure of NSD3-PWWP1 in complex with compound 3 Deposited 2018-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EH2 2-[(~{E})-2-thiophen-2-ylethenyl]benzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 2.10 Å R-free 0.235
6G25 X-ray structure of NSD3-PWWP1 in complex with compound 4 Deposited 2018-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EHQ 3,5-dimethyl-4-(4-pyridin-4-yl-1~{H}-pyrazol-3-yl)-1,2-oxazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.43 Å R-free 0.229
6G27 X-ray structure of NSD3-PWWP1 in complex with compound 5 Deposited 2018-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EHE 5-methyl-6-phenyl-2-piperidin-4-yl-pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.65 Å R-free 0.227
6G29 X-ray structure of NSD3-PWWP1 in complex with compound 6 Deposited 2018-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EHK 5-methyl-2-piperidin-4-yl-6-pyridin-4-yl-pyridazin-3-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.70 Å R-free 0.210
6G2B X-ray structure of NSD3-PWWP1 in complex with compound 8 Deposited 2018-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EH8 4-(3-methyl-5-phenyl-imidazol-4-yl)pyridine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.61 Å R-free 0.225
6G2C X-ray structure of NSD3-PWWP1 in complex with compound 9 Deposited 2018-03-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EHT 3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)-1,2-oxazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.76 Å R-free 0.230
6G2E X-ray structure of NSD3-PWWP1 in complex with compound 13 Deposited 2018-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EHH [3,5-dimethyl-4-(1-methyl-5-pyridin-4-yl-imidazol-4-yl)phenyl]methanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.85 Å R-free 0.252
6G2F X-ray structure of NSD3-PWWP1 in complex with compound 16 Deposited 2018-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EHW 4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-1,2-oxazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.74 Å R-free 0.211
6G2O X-ray structure of NSD3-PWWP1 in complex with compound BI-9321 Deposited 2018-03-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 263–398（136 aa）	Not recorded	EJE [4-[5-(7-fluoranylquinolin-4-yl)-1-methyl-imidazol-4-yl]-3,5-dimethyl-phenyl]methanamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；100mM Morpheus Buffer 3, 30% P550MME_P20K, 10% Morpheus Ethylene glycols	Resolution 1.81 Å R-free 0.224
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 247–398（152 aa） Fragment：UNP residues 247-398	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM TRIS pH 9.0, 23% PEG3350	Resolution 2.80 Å R-free 0.262
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 247–398（152 aa） Fragment：UNP residues 247-398	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM TRIS pH 9.0, 23% PEG3350	Resolution 2.80 Å R-free 0.262
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 247–398（152 aa） Fragment：UNP residues 247-398	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM TRIS pH 9.0, 23% PEG3350	Resolution 2.80 Å R-free 0.262
6G3P X-ray structure of seleno-methionine labelled NSD3-PWWP1 Deposited 2018-03-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 247–398（152 aa） Fragment：UNP residues 247-398	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；50 mM TRIS pH 9.0, 23% PEG3350	Resolution 2.80 Å R-free 0.262
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 247–398（152 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol	Resolution 2.53 Å R-free 0.274
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 247–398（152 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol	Resolution 2.53 Å R-free 0.274
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 247–398（152 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol	Resolution 2.53 Å R-free 0.274
6G3T X-ray structure of NSD3-PWWP1 Deposited 2018-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 247–398（152 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；100 mM HEPES pH 7.8, 28% PEG3350, 2% PEG200, 1.5% 1,2-Butandiol	Resolution 2.53 Å R-free 0.274
7CRP NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (1:1 binding mode) Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain I 680–1437（758 aa）	Mutation：E1181K, T1232A	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7CRQ NSD3 bearing E1181K/T1232A dual mutation in complex with 187-bp NCP (2:1 binding mode) Deposited 2020-08-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain I 680–1437（758 aa） Chain L 680–1437（758 aa）	Mutation：E1181K, T1232A Mutation：E1181K, T1232A	SAM S-ADENOSYLMETHIONINE × 2 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane	Resolution 3.15 Å
7CRR Native NSD3 bound to 187-bp nucleosome Deposited 2020-08-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain I 680–1437（758 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；blotted for 3 s before being plunged into liquid ethane	Resolution 3.48 Å
7JYN Solution NMR structure of human Brd3 ET complexed with NSD3(148-184) peptide Deposited 2020-08-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 148–184（37 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure 1 NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] NSD3(148-184), 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.25 mM NSD3(148-184), 0.25 mM U-100% 13C; U-100% 15 Brd3ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.25 mM [U-100% 13C; U-100% 15N] NSD3(148-184), 0.2 mM [U-100% 13C; U-100% 15N] Brd3ET, 100 mM sodium chloride, 20 mM sodium phosphate, 2 mM 2-mercaptoethanol, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided

24 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NSD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–107； UniProt 1310–1413 Author chain C； PDBConstruct 4–107； UniProt 1310–1413

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4gnd
Deposition date deposition_date	2012-08-17
Structure title title	Crystal Structure of NSD3 tandem PHD5-C5HCH domains
Keywords keywords	zinc finger, transcription, histone, nuclear protein, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.25 Å
Radius of gyration Rg (electron density) rg_electron	25.02 Å
Forward intensity I(0) i0	11769900.00
Molecular weight molecular_weight	23566.0 kDa
Excluded volume excluded_volume	28278 Å³
Envelope volume envelope_volume	42927 Å³
Hydration-shell volume shell_volume	15313 Å³
Envelope diameter envelope_diameter	92.6 Å
Shell Rg shell_rg	30.57 Å
Envelope Rg envelope_rg	25.02 Å
Shape Rg shape_rg	25.07 Å
Total Rg total_rg	25.58 Å
Total atoms total_atoms	1604
Residues n_residues	205
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.9 Å
Rg (real space) rg_real	25.45 Å
Rg uncertainty (real space) rg_real_error	1.16 Å
I(0) (real space) i0_real	1.1770e+07
I(0) uncertainty (real space) i0_real_error	1.8940e+05
Rg (reciprocal space) rg_reciprocal	25.39 Å
I(0) (reciprocal space) i0_reciprocal	11770000.0000
Solution quality estimate total_estimate	0.5469
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	20.4 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.618
Angular range angular_range	— – 0.3150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	492300.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.690; Stabil: 0.998; Sysdev: 0.242; Positv: 1.000; Valcen: 0.315; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase NSD3
Molecular weight formula_weight	12058.8 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	1629

SNARKIKTEPKQMHEDYCFQCGDGGELVMCDKKDCPKAYHLLCLNLTQPPYGKWECPWHQCDECSSAAVSFCEFCPHSFCKDHEKGALVPSALEGRLCCSEHDPMAP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	25

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4gndA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

Domain ID domain_id	4gndC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Unit-cell length a length_a	58.510 Å
Unit-cell length b length_b	58.510 Å
Unit-cell length c length_c	108.581 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	2.270 Å
Low-resolution limit resolution_low	50.670 Å
R factor r_factor	0.1751
R_work r_work	0.1716
R_free r_free	0.2190

fit	/app/data/saxs_computation/gn/4gnd/4gnd.fit
pddf	/app/data/pr_computation/gn/4gnd/4gnd.pr.out
profile	/app/data/saxs_computation/gn/4gnd/4gnd.dat