SAXSdb — 5chk

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

Avidin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AVID_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–128； UniProt 25–152

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	5chk
Deposition date deposition_date	2015-07-10
Structure title title	Crystal structure of avidin - HABA complex (hexagonal crystal form)
Keywords keywords	glycoprotein, complex; GLYCOPROTEIN
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.

5chk__assembly_1__model_1

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

Download this curve (.dat)

5chk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5chk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.56 Å
Rg (electron density)	22.26 Å
Total Rg	23.36 Å
Atom count	3912
Residues	484
Excluded volume	69086 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5chk__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 (4)

Entity 1 Entity 1 polymer

Description description	Avidin
Molecular weight formula_weight	14350.1 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	1029

ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYTTAVTATSNEIKESPLHGTENTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRLRTQKE

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid
Molecular weight formula_weight	242.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	51

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5chka_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

CATH v4.4 (1 domains)

Domain ID domain_id	5chkA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

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Unit-cell length a length_a	61.310 Å
Unit-cell length b length_b	61.310 Å
Unit-cell length c length_c	120.530 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 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	40.180 Å
R factor r_factor	0.1640
R_work r_work	0.1607
R_free r_free	0.2275

Crystal structure of avidin - HABA complex (hexagonal crystal form)

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

Avidin

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

5chk__assembly_1__model_1

5chk__assembly_1__model_1 | I(q)

5chk__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Crystal structure of avidin - HABA complex (hexagonal crystal form)

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

Avidin

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

5chk__assembly_1__model_1

5chk__assembly_1__model_1 | I(q)

5chk__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)