SAXSdb — 2omv

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

Internalin-A

Listeria monocytogenes

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Epithelial-cadherin × 1 （P12830） CALCIUM ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	INLA_LISMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–460； UniProt 36–495

Epithelial-cadherin

Homo sapiens

UniProt P12830

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Internalin-A × 1 （P25146） CALCIUM ION × 2 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CADH1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 6–105； UniProt 156–255

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	2omv
Deposition date deposition_date	2007-01-23
Structure title title	Crystal structure of InlA S192N Y369S/hEC1 complex
Keywords keywords	leucine-rich-repeat, invasion protein, IG-like domain, adhesion protein, CELL INVASION-CELL ADHESION COMPLEX; CELL INVASION/CELL ADHESION
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.

2omv__assembly_1__model_1

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

Download this curve (.dat)

2omv__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2omv__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.29 Å
Rg (electron density)	28.99 Å
Total Rg	29.39 Å
Atom count	4288
Residues	563
Excluded volume	76765 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2omv__assembly_1__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 (5)

Entity 1 Entity 1 polymer

Description description	Internalin-A
Molecular weight formula_weight	49778.6 kDa
Mutation mutation	S192N Y369S
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	5471

ATITQDTPINQIFTDTALAEKMKTVLGKTNVTDTVSQTDLDQVTTLQADRLGIKSIDGVEYLNNLTQINFSNNQLTDITPLKNLTKLVDILMNNNQIADITPLANLTNLTGLTLFNNQITDIDPLKNLTNLNRLELSSNTISDISALSGLTSLQQLNFGNQVTDLKPLANLTTLERLDISSNKVSDISVLAKLTNLESLIATNNQISDITPLGILTNLDELSLNGNQLKDIGTLASLTNLTDLDLANNQISNLAPLSGLTKLTELKLGANQISNISPLAGLTALTNLELNENQLEDISPISNLKNLTYLTLYFNNISDISPVSSLTKLQRLFFSNNKVSDVSSLANLTNINWLSAGHNQISDLTPLANLTRITQLGLNDQAWTNAPVNYKANVSIPNTVKNVTGALIAPATISDGGSYTEPDITWNLPSYTNEVSYTFSQPVTIGKGTTTFSGTVTQPLKA

Source Source

Source organism organism	Listeria monocytogenes
NCBI taxonomy ID ncbi_taxonomy_id	169963
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	Epithelial-cadherin
Molecular weight formula_weight	11523.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPLGSWVIPPISCPENEKGPFPKNLVQIKSNKDKEGKVFYSITGQGADTPPVGVFIIERETGWLKVTEPLDRERIATYTLFSHAVSSNGNAVEDPMEILITVTDQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli BL21

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	2

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	837

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2omva1
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.1.18.15 — Internalin Ig-like domain

Domain ID domain_id	d2omva2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Superfamily Superfamily superfamily	c.10.2 — L domain-like
Family Family family	c.10.2.1 — Internalin LRR domain

Domain ID domain_id	d2omva3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2omvb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.6 — Cadherin-like
Family Family family	b.1.6.1 — Cadherin

Domain ID domain_id	d2omvb3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	2omvA01
Class class	3 — Alpha Beta
Architecture architecture	80 — Alpha-Beta Horseshoe
Topology topology	10 — Leucine-rich repeat, LRR (right-handed beta-alpha superhelix)
Homologous superfamily homologous superfamily	10 — Ribonuclease Inhibitor

Domain ID domain_id	2omvA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1220 —

Domain ID domain_id	2omvB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	60 — Cadherins

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Unit-cell length a length_a	55.373 Å
Unit-cell length b length_b	87.377 Å
Unit-cell length c length_c	110.955 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	1.900 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.1570
R_work r_work	0.1530
R_free r_free	0.2190

Crystal structure of InlA S192N Y369S/hEC1 complex

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

Internalin-A

State in the Current Structure

Other States of the Same Protein in the Database

Epithelial-cadherin

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

2omv__assembly_1__model_1

2omv__assembly_1__model_1 | I(q)

2omv__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of InlA S192N Y369S/hEC1 complex

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

Internalin-A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Epithelial-cadherin

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

2omv__assembly_1__model_1

2omv__assembly_1__model_1 | I(q)

2omv__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (5 domains)

CATH v4.4 (3 domains)

7. Citations (1)