SAXSdb — 1kcc

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

ENDOPOLYGALACTURONASE

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	beta-D-galactopyranuronic acid × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 CHLORIDE ION × 1 SODIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P79074_9AGAR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–335； UniProt 25–359

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	1kcc
Deposition date deposition_date	2001-11-08
Structure title title	Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution.
Keywords keywords	BETA HELICAL STRUCTURE, GLYCOSIDE HYDROLASE, SILVER-LEAF INDUCING SUBSTANCE, HYDROLASE; HYDROLASE
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.

1kcc__assembly_1__model_1

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

Download this curve (.dat)

1kcc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kcc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.68 Å
Rg (electron density)	19.82 Å
Total Rg	20.72 Å
Atom count	2458
Residues	333
Excluded volume	43184 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kcc__assembly_1__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	ENDOPOLYGALACTURONASE
Molecular weight formula_weight	34652.4 kDa
EC 编号 ec_number	3.2.1.15
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	3130

ATCTVKSVDDAKDIAGCSAVTLNGFTVPAGNTLVLNPDKGATVTMAGDITFAKTTLDGPLFTIDGTGINFVGADHIFDGNGALYWDGKGTNNGTHKPHPFLKIKGSGTYKKFEVLNSPAQAISVGPTDAHLTLDGITVDDFAGDTKNLGHNTDGFDVSANNVTIQNCIVKNQDDCIAINDGNNIRFENNQCSGGHGISIGSIATGKHVSNVVIKGNTVTRSMYGVRIKAQRTATSASVSGVTYDANTISGIAKYGVLISQSYPDDVGNPGTGAPFSDVNFTGGATTIKVNNAATRVTVECGNCSGNWNWSQLTVTGGKAGTIKSDKAKITGGQYL

Entity 2 Entity 2 non-polymer

Description description	beta-D-galactopyranuronic acid
Molecular weight formula_weight	194.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 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	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	585

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1kcca_
Class class	b — All beta proteins
Fold Fold fold	b.80 — Single-stranded right-handed beta-helix
Superfamily Superfamily superfamily	b.80.1 — Pectin lyase-like
Family Family family	b.80.1.3 — Galacturonase

CATH v4.4 (1 domains)

Domain ID domain_id	1kccA00
Class class	2 — Mainly Beta
Architecture architecture	160 — 3 Solenoid
Topology topology	20 — Pectate Lyase C-like
Homologous superfamily homologous superfamily	10 — Single-stranded right-handed beta-helix, Pectin lyase-like

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Unit-cell length a length_a	46.515 Å
Unit-cell length b length_b	52.138 Å
Unit-cell length c length_c	37.187 Å
Unit-cell angle α angle_alpha	72.31 °
Unit-cell angle β angle_beta	69.09 °
Unit-cell angle γ angle_gamma	70.35 °
Molecules per unit cell Z z_pdb	1

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

Resolution resolution	1.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1140
R_work r_work	0.1094
R_free r_free	0.1364

Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution.

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

ENDOPOLYGALACTURONASE

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

1kcc__assembly_1__model_1

1kcc__assembly_1__model_1 | I(q)

1kcc__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (4)

Endopolygalacturonase I from Stereum purpureum complexed with a galacturonate at 1.00 A resolution.

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

ENDOPOLYGALACTURONASE

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

1kcc__assembly_1__model_1

1kcc__assembly_1__model_1 | I(q)

1kcc__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (4)