SAXSdb — 2vdb

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

SERUM ALBUMIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN × 1 （Q51911） DECANOIC ACID × 6 (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALBU_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–579； UniProt 30–608

PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN

PEPTOSTREPTOCOCCUS MAGNUS

UniProt Q51911

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	SERUM ALBUMIN × 1 （P02768） DECANOIC ACID × 6 (2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAB_PEPMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–55； UniProt 213–265

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	2vdb
Deposition date deposition_date	2007-10-04
Structure title title	Structure of human serum albumin with S-naproxen and the GA module
Keywords keywords	;LIPID-BINDING, METAL-BINDING, PROTEIN BINDING, PEPTIDOGLYCAN-ANCHOR, BACTERIAL ALBUMIN-BINDING, DISEASE MUTATION, THREE-HELIX BUNDLE, GA MODULE, DRUG BINDING, GLYCOPROTEIN, CLEAVAGE ON PAIR OF BASIC RESIDUES, HUMAN SERUM ALBUMIN, SECRETED, NAPROXEN, CELL WALL, GLYCATION ;; PROTEIN BINDING
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.

2vdb__assembly_1__model_1

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

Download this curve (.dat)

2vdb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2vdb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	28.91 Å
Rg (electron density)	27.97 Å
Total Rg	28.61 Å
Atom count	4872
Residues	629
Excluded volume	87047 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2vdb__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	SERUM ALBUMIN
Molecular weight formula_weight	65917.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4872

EVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPNLPRLVRPEVDVMCTAFHDNEETFLKKYLYEIARRHPYFYAPELLFFAKRYKAAFTECCQAADKAACLLPKLDELRDEGKASSAKQRLKCASLQKFGERAFKAWAVARLSQRFPKAEFAEVSKLVTDLTKVHTECCHGDLLECADDRADLAKYICENQDSISSKLKECCEKPLLEKSHCIAEVENDEMPADLPSLAADFVESKDVCKNYAEAKDVFLGMFLYEYARRHPDYSVVLLLRLAKTYETTLEKCCAAADPHECYAKVFDEFKPLVEEPQNLIKQNCELFEQLGEYKFQNALLVRYTKKVPQVSTPTLVEVSRNLGKVGSKCCKHPEAKRMPCAEDYLSVVLNQLCVLHEKTPVSDRVTKCCTESLVNRRPCFSALEVDETYVPKEFNAETFTFHADICTLSEKERQIKKQTALVELVKHKPKATKEQLKAVMDDFAAFVEKCCKADDKETCFAEEGKKLVAASQAALG

Entity 2 Entity 2 polymer

Description description	PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN
Molecular weight formula_weight	6209.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

HMTIDQWLLKNAKEDAIAELKKAGITSDFYFNAINKAKTVEEVNALKNEILKAHA

Source Source

Source organism organism	PEPTOSTREPTOCOCCUS MAGNUS
NCBI taxonomy ID ncbi_taxonomy_id	1260
Host organism host_organism	ESCHERICHIA COLI

Entity 3 Entity 3 non-polymer

Description description	DECANOIC ACID
Molecular weight formula_weight	172.3 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid
Molecular weight formula_weight	230.3 kDa
Source method src_method	syn
Copy count entity_count	1

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2vdba1
Class class	a — All alpha proteins
Fold Fold fold	a.126 — Serum albumin-like
Superfamily Superfamily superfamily	a.126.1 — Serum albumin-like
Family Family family	a.126.1.0 — automated matches

Domain ID domain_id	d2vdba2
Class class	a — All alpha proteins
Fold Fold fold	a.126 — Serum albumin-like
Superfamily Superfamily superfamily	a.126.1 — Serum albumin-like
Family Family family	a.126.1.0 — automated matches

Domain ID domain_id	d2vdba3
Class class	a — All alpha proteins
Fold Fold fold	a.126 — Serum albumin-like
Superfamily Superfamily superfamily	a.126.1 — Serum albumin-like
Family Family family	a.126.1.0 — automated matches

Domain ID domain_id	d2vdbb_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.2 — GA module, an albumin-binding domain

CATH v4.4 (7 domains)

Domain ID domain_id	2vdbA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vdbA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vdbA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vdbA04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vdbA05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vdbA06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2vdbB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	40 — Albumin-binding domain

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Unit-cell length a length_a	190.507 Å
Unit-cell length b length_b	49.462 Å
Unit-cell length c length_c	79.933 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.520 Å
Low-resolution limit resolution_low	94.920 Å
R factor r_factor	0.2360
R_work r_work	0.2340
R_free r_free	0.2800

Structure of human serum albumin with S-naproxen and the GA module

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

SERUM ALBUMIN

State in the Current Structure

Other States of the Same Protein in the Database

PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN

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

2vdb__assembly_1__model_1

2vdb__assembly_1__model_1 | I(q)

2vdb__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)

Structure of human serum albumin with S-naproxen and the GA module

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

SERUM ALBUMIN

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PEPTOSTREPTOCOCCAL ALBUMIN-BINDING PROTEIN

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

2vdb__assembly_1__model_1

2vdb__assembly_1__model_1 | I(q)

2vdb__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (4 domains)

CATH v4.4 (7 domains)

7. Citations (1)