SAXSdb — 4j4l

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

Internalin B,REPEAT MODULES,Variable lymphocyte receptor B

Eptatretus burgeri

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Interleukin-6 × 1 （P05231） water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Interleukin-6 × 1 （P05231） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A4L9V2_LISMN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–58； UniProt 43–100 Author chain B； PDBConstruct 1–58； UniProt 43–100

Internalin B,REPEAT MODULES,Variable lymphocyte receptor B

Eptatretus burgeri

UniProt Q4G1L3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Interleukin-6 × 1 （P05231） water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Interleukin-6 × 1 （P05231） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q4G1L3_EPTBU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 168–259； UniProt 141–232 Author chain B； PDBConstruct 168–259； UniProt 141–232

Interleukin-6

Homo sapiens

UniProt P05231

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 2	Internalin B,REPEAT MODULES,Variable lymphocyte receptor B × 1 （A4L9V2,Q4G1L3） water × 2	Consistent with protein count
2	Insufficient information	Heteromer	Protein 2	Internalin B,REPEAT MODULES,Variable lymphocyte receptor B × 1 （A4L9V2,Q4G1L3） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IL6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–168； UniProt 47–212 Author chain D； PDBConstruct 3–168； UniProt 47–212

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	4j4l
Deposition date deposition_date	2013-02-07
Structure title title	Modular evolution and design of the protein binding interface
Keywords keywords	LRR, IL-6 binding, Interleukin 6, extracellular matrix, PROTEIN BINDING-CYTOKINE complex; PROTEIN BINDING/CYTOKINE
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.

4j4l__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4j4l__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4j4l__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.40 Å
Rg (electron density)	23.16 Å
Total Rg	24.18 Å
Atom count	3312
Residues	417
Excluded volume	59285 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4j4l__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4j4l__assembly_2__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	Internalin B,REPEAT MODULES,Variable lymphocyte receptor B
Molecular weight formula_weight	30059.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6751

PIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLTLEPNQLQSLPNGVFDKLTNLKELQLWANQLQSLPDGVFDKLTNLTYLNLAFNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPKGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIICPTLEHHHHHH

Source Source

Source organism organism	Eptatretus burgeri
Common name common_name	Inshore hagfish
NCBI taxonomy ID ncbi_taxonomy_id	7764
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Interleukin-6
Molecular weight formula_weight	19196.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GSLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	158

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4j4lA00
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	4j4lB00
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	4j4lC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	4j4lD00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	46.319 Å
Unit-cell length b length_b	134.001 Å
Unit-cell length c length_c	148.722 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	61.090 Å
R factor r_factor	—
R_work r_work	0.2046
R_free r_free	0.2684

Modular evolution and design of the protein binding interface

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

Internalin B,REPEAT MODULES,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Internalin B,REPEAT MODULES,Variable lymphocyte receptor B

State in the Current Structure

Other States of the Same Protein in the Database

Interleukin-6

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

4j4l__assembly_2__model_1

4j4l__assembly_2__model_1 | I(q)

4j4l__assembly_2__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Modular evolution and design of the protein binding interface

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

Internalin B,REPEAT MODULES,Variable lymphocyte receptor 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

Internalin B,REPEAT MODULES,Variable lymphocyte receptor 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

Interleukin-6

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

4j4l__assembly_2__model_1

4j4l__assembly_2__model_1 | I(q)

4j4l__assembly_2__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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)