5vxj

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

Method: X-RAY DIFFRACTION

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

Invasin IpaD

Shigella flexneri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody JMK-E3 × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody JMK-E3 × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody JMK-E3 × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody JMK-E3 × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	single-domain antibody JMK-E3 × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IPAD_SHIFL
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–289； UniProt 38–322 Author chain C； PDBConstruct 5–289； UniProt 38–322 Author chain E； PDBConstruct 5–289； UniProt 38–322 Author chain G； PDBConstruct 5–289； UniProt 38–322 Author chain I； PDBConstruct 5–289； UniProt 38–322

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	5vxj
Deposition date deposition_date	2017-05-23
Structure title title	2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3
Keywords keywords	tip protein, VHH, T3SS, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

5vxj__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5vxj__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5vxj__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	25.61 Å
Rg (electron density)	25.08 Å
Total Rg	25.59 Å
Atom count	6000
Residues	396
Excluded volume	53532 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5vxj__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5vxj__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5vxj__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5vxj__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5vxj__assembly_5__model_1`	dimeric （2）	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)

Entity 1 Entity 1 polymer

Description description	Invasin IpaD
Molecular weight formula_weight	31904.6 kDa
Mutation mutation	C322S
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I
Atom count atom_count	29721

GSTGSHPVSSLTMLNDTLHNIRTTNQALKKELSQKTLTKTSLEEIALHSSQISMDVNKSAQLLDILSRNEYPINKDARELLHSAPKEAELDGDQMISHRELWAKIANSINDINEQYLKVYEHAVSSYTQMYQDFSAVLSSLAGWISPGGNDGNSVKLQVNSLKKALEELKEKYKDKPLYPANNTVSQEQANKWLTELGGTIGKVSQKNGGYVVSINMTPIDNMLKSLDNLGGNGEVVLDNAKYQAWNAGFSAEDETMKNNLQTLVQKYSNANSIFDNLVKVLSSTISSS

Source Source

Source organism organism	Shigella flexneri
NCBI taxonomy ID ncbi_taxonomy_id	623
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	single-domain antibody JMK-E3
Molecular weight formula_weight	15662.5 kDa
Source method src_method	man
Copy count entity_count	5

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J

GSTQVQLAETGGGLAQPGGSLRLSCAASGFTFSRAVMNWYRQAPGKERELVARIYDAGGNGSIADPVKGRFTISRDNAKNTVHLQMNSLKPEDTAMYVCNAGIFDGNYRTYWGQGTQVTVSSEPKTPKPQPARQGAPVPYPDPLEP

Source Source

Source organism organism	Vicugna pacos
NCBI taxonomy ID ncbi_taxonomy_id	30538
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	186

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

Domain ID domain_id	d5vxja_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

Domain ID domain_id	d5vxjb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5vxjc_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

Domain ID domain_id	d5vxjd_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5vxje_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

Domain ID domain_id	d5vxjf_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5vxjg_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

Domain ID domain_id	d5vxjh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5vxji_
Class class	a — All alpha proteins
Fold Fold fold	a.250 — IpaD-like
Superfamily Superfamily superfamily	a.250.1 — IpaD-like
Family Family family	a.250.1.1 — IpaD-like

Domain ID domain_id	d5vxjj_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	5vxjA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

Domain ID domain_id	5vxjC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

Domain ID domain_id	5vxjE00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

Domain ID domain_id	5vxjG00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

Domain ID domain_id	5vxjI00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1710 — IpaD-like
Homologous superfamily homologous superfamily	10 — IpaD-like

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Unit-cell length a length_a	79.014 Å
Unit-cell length b length_b	163.350 Å
Unit-cell length c length_c	216.021 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	20

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	45.048 Å
R factor r_factor	0.1995
R_work r_work	0.1964
R_free r_free	0.2590

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

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

Invasin IpaD

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

5vxj__assembly_3__model_1

5vxj__assembly_3__model_1 | I(q)

5vxj__assembly_3__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)

2.50 A resolution structure of IpaD from Shigella flexneri in complex with single-domain antibody JMK-E3

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

Invasin IpaD

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

5vxj__assembly_3__model_1

5vxj__assembly_3__model_1 | I(q)

5vxj__assembly_3__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

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (10 domains)

CATH v4.4 (5 domains)

7. Citations (1)