SAXSdb — 5u6a

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

Protein L

Finegoldia magna

UniProt Q51918

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Light Chain × 1 Heavy Chain × 1 Immunoglobulin G binding protein A × 1 （Q2UW42） meditope peptide × 1 MESO-ERYTHRITOL × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q51918_FINMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 5–63； UniProt 479–537

Immunoglobulin G binding protein A

Staphylococcus aureus

UniProt Q2UW42

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Light Chain × 1 Heavy Chain × 1 Protein L × 1 （Q51918） meditope peptide × 1 MESO-ERYTHRITOL × 1 water × 5	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q2UW42_STAAU
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain C； PDBConstruct 4–54； UniProt 74–124

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	5u6a
Deposition date deposition_date	2016-12-07
Structure title title	CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE
Keywords keywords	ANTIBODY, IMMUNE SYSTEM, ANTIBODY-DRUG CONJUGATES; 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.

5u6a__assembly_1__model_1

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

Download this curve (.dat)

5u6a__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5u6a__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.12 Å
Rg (electron density)	26.20 Å
Total Rg	27.00 Å
Atom count	4362
Residues	565
Excluded volume	76882 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5u6a__assembly_1__model_1`	pentameric （5）	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 (7)

Entity 1 Entity 1 polymer

Description description	Light Chain
Molecular weight formula_weight	23518.0 kDa
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	5469

DIQMTQSPILLSASVGDRVTITCRASQDVNTAVAWYQQRTNGSPRLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDEADYYCQQHYTTPPTFGAGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	Heavy Chain
Molecular weight formula_weight	23774.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQSPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAIYYCSRWGGDGFYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Source Source

Source organism organism	Homo sapiens
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Protein L
Molecular weight formula_weight	6850.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

SEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMNIKFAG

Source Source

Source organism organism	Finegoldia magna
Common name common_name	Peptostreptococcus magnus
NCBI taxonomy ID ncbi_taxonomy_id	1260
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Immunoglobulin G binding protein A
Molecular weight formula_weight	6037.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GSYNKDQQSAFYEILNMPNLNEAQRNGFIQSLKDDPSQSTNVLGEAKKLNESQA

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	meditope peptide
Molecular weight formula_weight	1851.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

XCQFDXSTXRLRCG

Entity 6 Entity 6 non-polymer

Description description	MESO-ERYTHRITOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	857

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6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

Domain ID domain_id	5u6aA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u6aA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u6aB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u6aC00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	5u6aE00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	53.250 Å
Unit-cell length b length_b	105.170 Å
Unit-cell length c length_c	117.070 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	1.736 Å
Low-resolution limit resolution_low	31.526 Å
R factor r_factor	0.1609
R_work r_work	0.1594
R_free r_free	0.1875

CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE

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

Protein L

State in the Current Structure

Other States of the Same Protein in the Database

Immunoglobulin G binding protein A

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

5u6a__assembly_1__model_1

5u6a__assembly_1__model_1 | I(q)

5u6a__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE

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

Protein L

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Immunoglobulin G binding protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5u6a__assembly_1__model_1

5u6a__assembly_1__model_1 | I(q)

5u6a__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 5 domains

CATH v4.4 (5 domains)

7. Citations (1)