SAXSdb — 1cvr

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

GINGIPAIN R

Porphyromonas gingivalis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide × 1 CALCIUM ION × 6 ZINC ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CPG2_PORGI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–435； UniProt 230–664

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	1cvr
Deposition date deposition_date	1999-08-24
Structure title title	Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)
Keywords keywords	CASPASES, CYSTEINE PROTEINASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
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.

1cvr__assembly_1__model_1

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

Download this curve (.dat)

1cvr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1cvr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.28 Å
Rg (electron density)	21.21 Å
Total Rg	22.18 Å
Atom count	3387
Residues	432
Excluded volume	60396 Å³
Maximum q	0.500 Å⁻¹

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

Entity 1 Entity 1 polymer

Description description	GINGIPAIN R
Molecular weight formula_weight	47932.8 kDa
EC 编号 ec_number	3.4.22.37
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3709

YTPVEEKENGRMIVIVAKKYEGDIKDFVDWKNQRGLRTEVKVAEDIASPVTANAIQQFVKQEYEKEGNDLTYVLLVGDHKDIPAKITPGIKSDQVYGQIVGNDHYNEVFIGRFSCESKEDLKTQIDRTIHYERNITTEDKWLGQALCIASAEGGPSADNGESDIQHENVIANLLTQYGYTKIIKCYDPGVTPKNIIDAFNGGISLVNYTGHGSETAWGTSHFGTTHVKQLTNSNQLPFIFDVACVNGDFLFSMPCFAEALMRAQKDGKPTGTVAIIASTIDQYWAPPMRGQDEMNEILCEKHPNNIKRTFGGVTMNGMFAMVEKYKKDGENMLDTWTVFGDPSLLVRTLVPTEMQVTAPANISASAQTFEVACDYNGAIATLSDDGDMVGTAIVKDGKAIIKLNESIADETNLTLTVVGYNKVTVIKDVKVEGTS

Source Source

Source organism organism	Porphyromonas gingivalis
NCBI taxonomy ID ncbi_taxonomy_id	837

Entity 2 Entity 2 non-polymer

Description description	D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-phenylalaninamide
Molecular weight formula_weight	501.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	322

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1cvra1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.12 — Gingipain R (RgpB), C-terminal domain

Domain ID domain_id	d1cvra2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.17 — Caspase-like
Superfamily Superfamily superfamily	c.17.1 — Caspase-like
Family Family family	c.17.1.2 — Gingipain R (RgpB), N-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1cvrA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10390 — Gingipain r; domain 1

Domain ID domain_id	1cvrA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1460 —

Domain ID domain_id	1cvrA03
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	51.930 Å
Unit-cell length b length_b	79.920 Å
Unit-cell length c length_c	99.820 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	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	—
R_work r_work	0.1630
R_free r_free	0.2070

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

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

GINGIPAIN R

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

1cvr__assembly_1__model_1

1cvr__assembly_1__model_1 | I(q)

1cvr__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of the Arg specific cysteine proteinase gingipain R (RGPB)

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

GINGIPAIN R

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

1cvr__assembly_1__model_1

1cvr__assembly_1__model_1 | I(q)

1cvr__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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)