SAXSdb — 4v2o

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

SAPOSIN-B

HOMO SAPIENS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAP_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–82； UniProt 195–273 Author chain B； PDBConstruct 4–82； UniProt 195–273 Author chain C； PDBConstruct 4–82； UniProt 195–273

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	4v2o
Deposition date deposition_date	2014-10-13
Structure title title	Structure of saposin B in complex with chloroquine
Keywords keywords	HYDROLASE ACTIVATOR, PROTEIN-LIGAND COMPLEX; HYDROLASE ACTIVATOR
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.

4v2o__assembly_1__model_1

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

Download this curve (.dat)

4v2o__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4v2o__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.12 Å
Rg (electron density)	15.69 Å
Total Rg	16.65 Å
Atom count	1227
Residues	159
Excluded volume	21837 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4v2o__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4v2o__assembly_2__model_1`	dimeric （2）	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	SAPOSIN-B
Molecular weight formula_weight	9097.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2040

GASGDVCQDCIQMVTDIQTAVRTNSTFVQALVEHVKEECDRLGPGMADICKNYISQYSEIAIQMMMHMQPKEICALVGFCDE

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	N4-(7-CHLORO-QUINOLIN-4-YL)-N1,N1-DIETHYL-PENTANE-1,4-DIAMINE
Molecular weight formula_weight	319.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d4v2oa_
Class class	a — All alpha proteins
Fold Fold fold	a.64 — Saposin-like
Superfamily Superfamily superfamily	a.64.1 — Saposin
Family Family family	a.64.1.3 — Saposin B

Domain ID domain_id	d4v2ob1
Class class	a — All alpha proteins
Fold Fold fold	a.64 — Saposin-like
Superfamily Superfamily superfamily	a.64.1 — Saposin
Family Family family	a.64.1.3 — Saposin B

Domain ID domain_id	d4v2ob2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4v2oc1
Class class	a — All alpha proteins
Fold Fold fold	a.64 — Saposin-like
Superfamily Superfamily superfamily	a.64.1 — Saposin
Family Family family	a.64.1.3 — Saposin B

Domain ID domain_id	d4v2oc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	4v2oA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	225 — NK-Lysin
Homologous superfamily homologous superfamily	10 — Saposin-like

Domain ID domain_id	4v2oB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	225 — NK-Lysin
Homologous superfamily homologous superfamily	10 — Saposin-like

Domain ID domain_id	4v2oC00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	225 — NK-Lysin
Homologous superfamily homologous superfamily	10 — Saposin-like

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Unit-cell length a length_a	75.299 Å
Unit-cell length b length_b	75.299 Å
Unit-cell length c length_c	94.716 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	18

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2303
R_work r_work	0.2290
R_free r_free	0.2538

Structure of saposin B in complex with chloroquine

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

SAPOSIN-B

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

4v2o__assembly_1__model_1

4v2o__assembly_1__model_1 | I(q)

4v2o__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) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Structure of saposin B in complex with chloroquine

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

SAPOSIN-B

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

4v2o__assembly_1__model_1

4v2o__assembly_1__model_1 | I(q)

4v2o__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) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)