SAXSdb — 1qkz

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

PROTEIN G-PRIME

STREPTOCOCCUS SP.

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	ANTIBODY × 1 ANTIBODY × 1 MAJOR OUTER MEMBRANE PROTEIN P1.16 × 1 （Q06140） water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q54181
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–64； UniProt 56–118

MAJOR OUTER MEMBRANE PROTEIN P1.16

OrganismNot specified

UniProt Q06140

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PROTEIN G-PRIME × 1 （Q54181） ANTIBODY × 1 ANTIBODY × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q06140
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–10； UniProt 4–13

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	1qkz
Deposition date deposition_date	1999-08-17
Structure title title	Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G
Keywords keywords	IMMUNE SYSTEM, FAB, PORA, NEISSERIA MENINGITIDIS, PORIN; 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.

1qkz__assembly_1__model_1

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

Download this curve (.dat)

1qkz__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1qkz__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.33 Å
Rg (electron density)	26.30 Å
Total Rg	27.10 Å
Atom count	3843
Residues	501
Excluded volume	67916 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1qkz__assembly_1__model_1`	tetrameric （4）	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	PROTEIN G-PRIME
Molecular weight formula_weight	7012.8 kDa
Mutation mutation	YES
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	4369

MTPAVTTYKLVINGKTLKGETTTKAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEKPE

Source Source

Source organism organism	STREPTOCOCCUS SP.
NCBI taxonomy ID ncbi_taxonomy_id	1320
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 polymer

Description description	ANTIBODY
Molecular weight formula_weight	23755.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

DVKLVESGGGLVKPGRSLKLSCAASGFTFSDYYMFWVRQTPEQRLEWVATISDGGAYTYYPDSVKGRFTISRDNAKNNLYLQMNSLKSEDTGMYYCARDPLEYYGMDYWGQGTSVAVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVNVTSSTWPSQSITCNVAHPASSTKVDKKIVPR

Entity 3 Entity 3 polymer

Description description	ANTIBODY
Molecular weight formula_weight	23954.6 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

NIVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYTVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHFPTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGKERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE

Entity 4 Entity 4 polymer

Description description	MAJOR OUTER MEMBRANE PROTEIN P1.16
Molecular weight formula_weight	888.9 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ANGGASGQVK

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	526

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d1qkza_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamily	d.15.7 — Immunoglobulin-binding domains
Family Family family	d.15.7.1 — Immunoglobulin-binding domains

Domain ID domain_id	d1qkzh1
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	d1qkzh2
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.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d1qkzl1
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	d1qkzl2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id	1qkzA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1qkzH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1qkzH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1qkzL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1qkzL02
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	43.482 Å
Unit-cell length b length_b	63.099 Å
Unit-cell length c length_c	89.374 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	81.54 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2090
R_work r_work	0.2050
R_free r_free	0.2620

Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G

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

PROTEIN G-PRIME

State in the Current Structure

Other States of the Same Protein in the Database

MAJOR OUTER MEMBRANE PROTEIN P1.16

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

1qkz__assembly_1__model_1

1qkz__assembly_1__model_1 | I(q)

1qkz__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)

Fab fragment (MN14C11.6) in complex with a peptide antigen derived from Neisseria meningitidis P1.7 serosubtype antigen and domain II from Streptococcal protein G

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

PROTEIN G-PRIME

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

MAJOR OUTER MEMBRANE PROTEIN P1.16

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

1qkz__assembly_1__model_1

1qkz__assembly_1__model_1 | I(q)

1qkz__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

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

CATH v4.4 (5 domains)

7. Citations (1)