1iwd

Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.

Method: X-RAY DIFFRACTION

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

ERVATAMIN B

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	THIOSULFATE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ERVB_TABDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–215； UniProt 1–215

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	1iwd
Deposition date deposition_date	2002-05-02
Structure title title	Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.
Keywords keywords	Cysteine protease, alpha-beta protein, catalytic dyad, L-domain, R-domain., 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.

1iwd__assembly_1__model_1

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

Download this curve (.dat)

1iwd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1iwd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.29 Å
Rg (electron density)	16.20 Å
Total Rg	17.20 Å
Atom count	1637
Residues	215
Excluded volume	28638 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1iwd__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 (3)

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1iwda_
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 (1 domains)

Domain ID domain_id	1iwdA00
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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Unit-cell length a length_a	48.200 Å
Unit-cell length b length_b	58.760 Å
Unit-cell length c length_c	69.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.630 Å
Low-resolution limit resolution_low	14.940 Å
R factor r_factor	0.1610
R_work r_work	0.1610
R_free r_free	0.1840

Description description	ERVATAMIN B
Molecular weight formula_weight	23200.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1845

Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.

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

ERVATAMIN 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

1iwd__assembly_1__model_1

1iwd__assembly_1__model_1 | I(q)

1iwd__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Description description	THIOSULFATE
Molecular weight formula_weight	112.1 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

Proposed Amino Acid Sequence and the 1.63 Angstrom X-ray Crystal Structure of a Plant Cysteine Protease Ervatamin B: Insight into the Structural Basis of its Stability and Substrate Specificity.

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

ERVATAMIN 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

1iwd__assembly_1__model_1

1iwd__assembly_1__model_1 | I(q)

1iwd__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

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)