SAXSdb — 6p4v

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

Deoxyhypusine synthase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 1-GUANIDINIUM-7-AMINOHEPTANE × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHYS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–372； UniProt 1–369 Author chain B； PDBConstruct 4–372； UniProt 1–369

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6p4v
Deposition date deposition_date	2019-05-28
Structure title title	1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7
Keywords keywords	Deoxyhypusine, NAD cofactor, hypusine, spermidine, GC7, transferase, TRANSFERASE-INHIBITOR complex; TRANSFERASE/INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6p4v__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6p4v__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p4v__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	31.86 Å
Rg (electron density)	30.91 Å
Total Rg	31.66 Å
Atom count	10478
Residues	1320
Excluded volume	186510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p4v__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Deoxyhypusine synthase
Molecular weight formula_weight	41213.6 kDa
EC 编号 ec_number	2.5.1.46
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5618

GGSMEGSLEREAPAGALAAVLKHSSTLPPESTQVRGYDFNRGVNYRALLEAFGTTGFQATNFGRAVQQVNAMIEKKLEPLSQDEDQHADLTQSRRPLTSCTIFLGYTSNLISSGIRETIRYLVQHNMVDVLVTTAGGVEEDLIKCLAPTYLGEFSLRGKELRENGINRIGNLLVPNENYCKFEDWLMPILDQMVMEQNTEGVKWTPSKMIARLGKEINNPESVYYWAQKNHIPVFSPALTDGSLGDMIFFHSYKNPGLVLDIVEDLRLINTQAIFAKCTGMIILGGGVVKHHIANANLMRNGADYAVYINTAQEFDGSDSGARPDEAVSWGKIRVDAQPVKVYADASLVFPLLVAETFAQKMDAFMHEKNED

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Molecular weight formula_weight	663.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1-GUANIDINIUM-7-AMINOHEPTANE
Molecular weight formula_weight	174.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	326

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d6p4va_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.1 — Deoxyhypusine synthase, DHS

Domain ID domain_id	d6p4vb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.31 — DHS-like NAD/FAD-binding domain
Superfamily Superfamily superfamily	c.31.1 — DHS-like NAD/FAD-binding domain
Family Family family	c.31.1.1 — Deoxyhypusine synthase, DHS

CATH v4.4 (2 domains)

Domain ID domain_id	6p4vA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	910 — Deoxyhypusine Synthase
Homologous superfamily homologous superfamily	10 — Deoxyhypusine synthase

Domain ID domain_id	6p4vB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	910 — Deoxyhypusine Synthase
Homologous superfamily homologous superfamily	10 — Deoxyhypusine synthase

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Unit-cell length a length_a	104.466 Å
Unit-cell length b length_b	104.466 Å
Unit-cell length c length_c	159.490 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	43.730 Å
R factor r_factor	0.1620
R_work r_work	0.1610
R_free r_free	0.1750

1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7

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

Deoxyhypusine synthase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6p4v__assembly_1__model_1

6p4v__assembly_1__model_1 | I(q)

6p4v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

1.65 Angstrom ternary complex of Deoxyhypusine synthase with cofactor NAD and spermidine mimic inhibitor GC7

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

Deoxyhypusine synthase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6p4v__assembly_1__model_1

6p4v__assembly_1__model_1 | I(q)

6p4v__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)