SAXSdb — 3gcd

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

RTX toxin RtxA

Vibrio cholerae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate × 1 INOSITOL HEXAKISPHOSPHATE × 1 SODIUM ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate × 1 INOSITOL HEXAKISPHOSPHATE × 1 SODIUM ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate × 1 INOSITOL HEXAKISPHOSPHATE × 1 SODIUM ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate × 1 INOSITOL HEXAKISPHOSPHATE × 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	Q9KS12_VIBCH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–209； UniProt 3442–3650 Author chain B； PDBConstruct 1–209； UniProt 3442–3650 Author chain C； PDBConstruct 1–209； UniProt 3442–3650 Author chain D； PDBConstruct 1–209； UniProt 3442–3650

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	3gcd
Deposition date deposition_date	2009-02-21
Structure title title	Structure of the V. cholerae RTX cysteine protease domain in complex with an aza-Leucine peptide inhibitor
Keywords keywords	V. cholerae, repeats-in-toxin, MARTX, cysteine protease, inositol hexakisphosphate, aza-peptide, aza-Leu, TOXIN-INHIBITOR complex; TOXIN/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.

3gcd__assembly_1__model_1

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

Download this curve (.dat)

3gcd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3gcd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.00 Å
Rg (electron density)	15.66 Å
Total Rg	16.62 Å
Atom count	1633
Residues	202
Excluded volume	28372 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3gcd__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3gcd__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3gcd__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3gcd__assembly_4__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	RTX toxin RtxA
Molecular weight formula_weight	22709.9 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	6677

ADGKILHNQNVNSWGPITVTPTTDGGETRFDGQIIVQMENDPVVAKAAANLAGKHAESSVVVQLDSDGNYRVVYGDPSKLDGKLRWQLVGHGRDHSETNNTRLSGYSADELAVKLAKFQQSFNQAENINNKPDHISIVGCSLVSDDKQKGFGHQFINAMDANGLRVDVSVRSSELAVDEAGRKHTKDANGDWVQKAENNKVSLSWDAQG

Source Source

Source organism organism	Vibrio cholerae
NCBI taxonomy ID ncbi_taxonomy_id	666
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ethyl (5S,8S,14S)-14-hydroxy-5,8,11-tris(2-methylpropyl)-3,6,9,12-tetraoxo-1-phenyl-2-oxa-4,7,10,11-tetraazapentadecan-15-oate
Molecular weight formula_weight	592.7 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	145

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3gcdA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11050 — MARTX cysteine protease (CPD) domain

Domain ID domain_id	3gcdB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11050 — MARTX cysteine protease (CPD) domain

Domain ID domain_id	3gcdC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11050 — MARTX cysteine protease (CPD) domain

Domain ID domain_id	3gcdD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	11050 — MARTX cysteine protease (CPD) domain

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Unit-cell length a length_a	48.560 Å
Unit-cell length b length_b	65.854 Å
Unit-cell length c length_c	254.880 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	16

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

Resolution resolution	2.350 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2206
R_work r_work	0.2183
R_free r_free	0.2650

Structure of the V. cholerae RTX cysteine protease domain in complex with an aza-Leucine peptide inhibitor

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

RTX toxin RtxA

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

3gcd__assembly_1__model_1

3gcd__assembly_1__model_1 | I(q)

3gcd__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of the V. cholerae RTX cysteine protease domain in complex with an aza-Leucine peptide inhibitor

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

RTX toxin RtxA

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

3gcd__assembly_1__model_1

3gcd__assembly_1__model_1 | I(q)

3gcd__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)