SAXSdb — 1cqd

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

PROTEIN (PROTEASE II)

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–221	Not recorded	beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 THJ THIOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.2；0.1 M SODIUM ACETATE BUFFER (PH 5.2) CONTAINING 0.1 M AMMONIUM SULFATE, 26% POLYETHYLENE GLYCOL MONOMETHYLETHER 2000, AND 2.5 MM SODIUM TETRATHIONATE	Resolution 2.10 Å R-free 0.249
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–221	Not recorded	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 THJ THIOSULFATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.2；0.1 M SODIUM ACETATE BUFFER (PH 5.2) CONTAINING 0.1 M AMMONIUM SULFATE, 26% POLYETHYLENE GLYCOL MONOMETHYLETHER 2000, AND 2.5 MM SODIUM TETRATHIONATE	Resolution 2.10 Å R-free 0.249
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–221	Not recorded	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 THJ THIOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.2；0.1 M SODIUM ACETATE BUFFER (PH 5.2) CONTAINING 0.1 M AMMONIUM SULFATE, 26% POLYETHYLENE GLYCOL MONOMETHYLETHER 2000, AND 2.5 MM SODIUM TETRATHIONATE	Resolution 2.10 Å R-free 0.249
4	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–221	Not recorded	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 THJ THIOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.2；0.1 M SODIUM ACETATE BUFFER (PH 5.2) CONTAINING 0.1 M AMMONIUM SULFATE, 26% POLYETHYLENE GLYCOL MONOMETHYLETHER 2000, AND 2.5 MM SODIUM TETRATHIONATE	Resolution 2.10 Å R-free 0.249

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	CPGP2_ZINOF
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 1–221 Author chain B； PDBConstruct 1–221； UniProt 1–221 Author chain C； PDBConstruct 1–221； UniProt 1–221 Author chain D； PDBConstruct 1–221； UniProt 1–221

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	1cqd
Deposition date deposition_date	1999-06-15
Structure title title	THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE
Keywords keywords	CYSTEINE PROTEASE, GLYCOPROTEIN, PROLINE SPECIFICITY, CARBOHYDRATE, PAPAIN FAMILY, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.38 Å
Radius of gyration Rg (electron density) rg_electron	32.20 Å
Forward intensity I(0) i0	165559000.00
Molecular weight molecular_weight	96871.0 kDa
Excluded volume excluded_volume	118590 Å³
Envelope volume envelope_volume	152250 Å³
Hydration-shell volume shell_volume	40718 Å³
Envelope diameter envelope_diameter	114.0 Å
Shell Rg shell_rg	38.05 Å
Envelope Rg envelope_rg	31.56 Å
Shape Rg shape_rg	32.20 Å
Total Rg total_rg	32.62 Å
Total atoms total_atoms	6798
Residues n_residues	864
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	108.5 Å
Rg (real space) rg_real	32.41 Å
Rg uncertainty (real space) rg_real_error	0.77 Å
I(0) (real space) i0_real	1.6560e+08
I(0) uncertainty (real space) i0_real_error	2.7440e+06
Rg (reciprocal space) rg_reciprocal	32.40 Å
I(0) (reciprocal space) i0_reciprocal	165600000.0000
Solution quality estimate total_estimate	0.6936
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.1 Å
Skewness Skewness skewness	0.399
Kurtosis Kurtosis kurtosis	-0.135
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	33000000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.810; Stabil: 1.000; Sysdev: 0.242; Positv: 1.000; Valcen: 0.993; Smooth: 0.863

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PROTEASE II)
Molecular weight formula_weight	23941.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7171

DDLPDSIDWRENGAVVPVKNQGGCGSCWAFSTVAAVEGINQIVTGDLISLSEQQLVDCTTANHGCRGGWMNPAFQFIVNNGGINSEETYPYRGQDGICNSTVNAPVVSIDSYENVPSHNEQSLQKAVANQPVSVTMDAAGRDFQLYRSGIFTGSCNISANHALTVVGYGTENDKDFWIVKNSWGKNWGESGYIRAERNIENPDGKCGITRFASYPVKKGTN

Entity 2 Entity 2 branched

Description description	beta-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 branched

Description description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	THIOSULFATE
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 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 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	373

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1cqda_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1cqdb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1cqdc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

Domain ID domain_id	d1cqdd_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.3 — Cysteine proteinases
Superfamily Superfamily superfamily	d.3.1 — Cysteine proteinases
Family Family family	d.3.1.1 — Papain-like

CATH v4.4 (4 domains)

Domain ID domain_id	1cqdA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	1cqdB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	1cqdC00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

Domain ID domain_id	1cqdD00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily	10 — Cysteine proteinases

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8. Citations (1)

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Unit-cell length a length_a	93.980 Å
Unit-cell length b length_b	45.450 Å
Unit-cell length c length_c	110.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.03 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	0.2130
R_work r_work	0.2130
R_free r_free	0.2490

fit	/app/data/saxs_computation/cq/1cqd/1cqd.fit
pddf	/app/data/pr_computation/cq/1cqd/1cqd.pr.out
profile	/app/data/saxs_computation/cq/1cqd/1cqd.dat

THE 2.1 ANGSTROM STRUCTURE OF A CYSTEINE PROTEASE WITH PROLINE SPECIFICITY FROM GINGER RHIZOME, ZINGIBER OFFICINALE