SAXSdb — 3wcd

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

Squalene 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 6	2-(4-phenoxyphenoxy)ethyl thiocyanate × 4 water × 6	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	2-(4-phenoxyphenoxy)ethyl thiocyanate × 2 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 3	2-(4-phenoxyphenoxy)ethyl thiocyanate × 2 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FDFT_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–360； UniProt 31–370 Author chain B； PDBConstruct 21–360； UniProt 31–370 Author chain C； PDBConstruct 21–360； UniProt 31–370 Author chain D； PDBConstruct 21–360； UniProt 31–370 Author chain E； PDBConstruct 21–360； UniProt 31–370 Author chain F； PDBConstruct 21–360； UniProt 31–370

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	3wcd
Deposition date deposition_date	2013-05-27
Structure title title	The complex structure of HsSQS wtih ligand, WC-9
Keywords keywords	isoprenoids, drug discovery, TRANSFERASE, WC-9; TRANSFERASE
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.

3wcd__assembly_1__model_1

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

Download this curve (.dat)

3wcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3wcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.19 Å
Rg (electron density)	39.46 Å
Total Rg	39.76 Å
Atom count	16252
Residues	2004
Excluded volume	290320 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3wcd__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3wcd__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3wcd__assembly_3__model_1`	trimeric （3）	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 (3)

Entity 1 Entity 1 polymer

Description description	Squalene synthase
Molecular weight formula_weight	41289.0 kDa
EC 编号 ec_number	2.5.1.21
Mutation mutation	K248L, K315L, K318L
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	17020

MGSSHHHHHHSSGLVPRGSHMDQDSLSSSLKTCYKYLNQTSRSFAAVIQALDGEMRNAVCIFYLVLRALDTLEDDMTISVEKKVPLLHNFHSFLYQPDWRFMESKEKDRQVLEDFPTISLEFRNLAEKYQTVIADICRRMGIGMAEFLDKHVTSEQEWDKYCHYVAGLVGIGLSRLFSASEFEDPLVGEDTERANSMGLFLQKTNIIRDYLEDQQGGREFWPQEVWSRYVKKLGDFALPENIDLAVQCLNELITNALHHIPDVITYLSRLRNQSVFNFCAIPQVMAIATLAACYNNQQVFKGAVLIRLGQAVTLMMDATNMPAVKAIIYQYMEEIYHRIPDSNPSSSKTRQIISTIRTQN

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	2-(4-phenoxyphenoxy)ethyl thiocyanate
Molecular weight formula_weight	271.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	768

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d3wcda_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.2 — Squalene synthase

Domain ID domain_id	d3wcdb_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.2 — Squalene synthase

Domain ID domain_id	d3wcdc_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.2 — Squalene synthase

Domain ID domain_id	d3wcdd_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.2 — Squalene synthase

Domain ID domain_id	d3wcde_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.2 — Squalene synthase

Domain ID domain_id	d3wcdf_
Class class	a — All alpha proteins
Fold Fold fold	a.128 — Terpenoid synthases
Superfamily Superfamily superfamily	a.128.1 — Terpenoid synthases
Family Family family	a.128.1.2 — Squalene synthase

CATH v4.4 (6 domains)

Domain ID domain_id	3wcdA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	3wcdB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	3wcdC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	3wcdD00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	3wcdE00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

Domain ID domain_id	3wcdF00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	600 — Farnesyl Diphosphate Synthase
Homologous superfamily homologous superfamily	10 — Farnesyl Diphosphate Synthase

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Unit-cell length a length_a	85.728 Å
Unit-cell length b length_b	153.744 Å
Unit-cell length c length_c	91.431 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.99 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.1830
R_free r_free	0.2340

The complex structure of HsSQS wtih ligand, WC-9

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

Squalene 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

3wcd__assembly_1__model_1

3wcd__assembly_1__model_1 | I(q)

3wcd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

The complex structure of HsSQS wtih ligand, WC-9

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

Squalene 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

3wcd__assembly_1__model_1

3wcd__assembly_1__model_1 | I(q)

3wcd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)