SAXSdb — 5u3d

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain E； UniProt 477–537	Not recorded	MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E × 1 MEMAB TRASTUZUMAB FAB HEAVY CHAIN × 1 Immunoglobulin G binding protein A × 1 （Q2UW42） MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 MM TRIS, PH 7.2, 50 MM NACL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.77 Å R-free 0.185

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5U3D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HEZ Structure of P. magnus protein L bound to a human IgM Fab. Deposited 2000-11-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 476–536（61 aa） Fragment：820-880	Not recorded	IMD IMIDAZOLE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；13-16% MPEG 5000, 100MM IMIDAZOLE MALATE, PH8.5, pH 8.50	Resolution 2.70 Å R-free 0.278
1YMH anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W Deposited 2005-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 474–538（65 aa）	Mutation：A866W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；293 K；9% PEG5K, 100mM Na cacodylate, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.302
1YMH anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W Deposited 2005-01-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 474–538（65 aa）	Mutation：A866W	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.1；293 K；9% PEG5K, 100mM Na cacodylate, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.302
2FS1 solution structure of PSD-1 Deposited 2006-01-20	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 798–839（42 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 50 mM；Pressure ambient NMR sample composition 0.2~0.4 mM PSD-1, 50 mM sodium phosphate buffer, pH 7.0, 0.1 mM EDTA, 10% D2O, 90% H2O \| 10% D2O, 90% H2O	Resolution not provided
4IOI Meditope-enabled trastuzumab in complex with CQFDLSTRRLKC Deposited 2013-01-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 476–537（62 aa）	Mutation：T34I, D55A, Y73N, T74H, I75M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；20% PEG 3350, 25 mM NaCl, 50 mM Hepes, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.204
5U5F MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT IN COMPLEX WITH (Ac) CQFDA(PH)2STRRLRCGGSK Deposited 2016-12-06	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 477–537（61 aa）	Mutation：YES	MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 MM TRIS, PH 7.2, 50 MM NACL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.81 Å R-free 0.192
5U5M CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-MEDITOPE Deposited 2016-12-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 477–537（61 aa）	Not recorded	MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；18 % PEG 3350, 150 MM NACL, 100 MM TRIS, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.88 Å R-free 0.197
5U6A CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE Deposited 2016-12-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 479–537（59 aa）	Not recorded	MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 3350 200 MM NACL, PH 7.2	Resolution 1.74 Å R-free 0.188
6B9Y Trastuzumab Fab v3 in complex with 5-phenyl meditope variant Deposited 2017-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 477–537（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 15% PEG3350, 24 mM NaCl	Resolution 2.14 Å R-free 0.218
6B9Z Trastuzumab Fab v3 Deposited 2017-10-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 477–537（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG3350	Resolution 1.82 Å R-free 0.189
6BAE Trastuzumab Fab v3 in complex with CQFDLSTRRLKC Deposited 2017-10-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 477–537（61 aa）	Mutation：T17I, D38A, Y56N, T57H, I58M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 24 mM NaCl, 15% PEG 3350	Resolution 2.14 Å R-free 0.224
6BAH Trastuzumab Fab v3 with 5-diphenyl meditope variant Deposited 2017-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 477–537（61 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG 3350	Resolution 1.90 Å R-free 0.194

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q51918_FINMA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain E； PDBConstruct 5–65； UniProt 477–537

Immunoglobulin G binding protein A

Staphylococcus aureus

UniProt Q2UW42

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 74–124	Not recorded	MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E × 1 MEMAB TRASTUZUMAB FAB HEAVY CHAIN × 1 Protein L × 1 （Q51918） MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 MM TRIS, PH 7.2, 50 MM NACL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.77 Å R-free 0.185

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5U3D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5U5F MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT IN COMPLEX WITH (Ac) CQFDA(PH)2STRRLRCGGSK Deposited 2016-12-06	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 74–124（51 aa）	Mutation：YES	MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 MM TRIS, PH 7.2, 50 MM NACL, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.81 Å R-free 0.192
5U5M CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-MEDITOPE Deposited 2016-12-06	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 74–124（51 aa）	Not recorded	MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；18 % PEG 3350, 150 MM NACL, 100 MM TRIS, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K	Resolution 1.88 Å R-free 0.197
5U6A CRYSTAL STRUCTURE OF I83E MEDITOPE-ENABLED TRASTUZUMAB WITH AZIDO-PEG3-MEDITOPE Deposited 2016-12-07	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 74–124（51 aa）	Not recorded	MRY MESO-ERYTHRITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 3350 200 MM NACL, PH 7.2	Resolution 1.74 Å R-free 0.188
6B9Y Trastuzumab Fab v3 in complex with 5-phenyl meditope variant Deposited 2017-10-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 74–124（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 15% PEG3350, 24 mM NaCl	Resolution 2.14 Å R-free 0.218
6B9Z Trastuzumab Fab v3 Deposited 2017-10-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 74–124（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG3350	Resolution 1.82 Å R-free 0.189
6BAE Trastuzumab Fab v3 in complex with CQFDLSTRRLKC Deposited 2017-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 74–124（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 24 mM NaCl, 15% PEG 3350	Resolution 2.14 Å R-free 0.224
6BAH Trastuzumab Fab v3 with 5-diphenyl meditope variant Deposited 2017-10-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 74–124（51 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG 3350	Resolution 1.90 Å R-free 0.194

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

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	5u3d
Deposition date deposition_date	2016-12-01
Structure title title	STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT
Keywords keywords	IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	28.46 Å
Radius of gyration Rg (electron density) rg_electron	27.59 Å
Forward intensity I(0) i0	61309400.00
Molecular weight molecular_weight	59920.0 kDa
Excluded volume excluded_volume	74405 Å³
Envelope volume envelope_volume	94561 Å³
Hydration-shell volume shell_volume	29338 Å³
Envelope diameter envelope_diameter	94.9 Å
Shell Rg shell_rg	33.92 Å
Envelope Rg envelope_rg	27.45 Å
Shape Rg shape_rg	27.58 Å
Total Rg total_rg	28.25 Å
Total atoms total_atoms	4220
Residues n_residues	552
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	91.0 Å
Rg (real space) rg_real	28.44 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	6.1310e+07
I(0) uncertainty (real space) i0_real_error	8.4480e+05
Rg (reciprocal space) rg_reciprocal	28.45 Å
I(0) (reciprocal space) i0_reciprocal	61310000.0000
Solution quality estimate total_estimate	0.8932
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.5 Å
Skewness Skewness skewness	0.291
Kurtosis Kurtosis kurtosis	-0.389
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7938000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.811

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	MEMAB TRASTUZUMAB FAB LIGHT CHAIN I83E
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	5161

DIQMTQSPILLSASVGDRVTITCRASQDVNTAVAWYQQRTNGSPRLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDEADYYCQQHYTTPPTFGAGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 2 Entity 2 polymer

Description description	MEMAB TRASTUZUMAB FAB 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

来源 Source

来源生物 organism	Homo sapiens
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Cricetulus griseus

Entity 3 Entity 3 polymer

Description description	Protein L
Molecular weight formula_weight	6994.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

SGSEVTIKVNLIFADGKIQTAEFKGTFEEATAEAYRYAALLAKVNGEYTADLEDGGNHMNIKFAG

来源 Source

来源生物 organism	Finegoldia magna
通用名 common_name	Peptostreptococcus magnus
NCBI Class编号 ncbi_taxonomy_id	1260
宿主生物 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

来源 Source

来源生物 organism	Staphylococcus aureus
NCBI Class编号 ncbi_taxonomy_id	1280
宿主生物 host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	803

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

Domain ID domain_id	d5u3da1
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.1.1.0 — automated matches

Domain ID domain_id	d5u3da2
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	d5u3db_
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	d5u3dc1
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

Domain ID domain_id	d5u3dc2
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	d5u3de1
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	d5u3de2
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 (5 domains)

Domain ID domain_id	5u3dA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u3dA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u3dB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5u3dC00
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	5u3dE00
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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8. Citations (1)

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Unit-cell length a length_a	52.850 Å
Unit-cell length b length_b	104.650 Å
Unit-cell length c length_c	116.880 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	1.770 Å
Low-resolution limit resolution_low	33.430 Å
R factor r_factor	0.1580
R_work r_work	0.1570
R_free r_free	0.1850

fit	/app/data/saxs_computation/u3/5u3d/5u3d.fit
pddf	/app/data/pr_computation/u3/5u3d/5u3d.pr.out
profile	/app/data/saxs_computation/u3/5u3d/5u3d.dat

STRUCTURE OF MEDITOPE ENABLED TRASTUZUMAB I83E VARIANT

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 polymer

Polymer Polymer

来源 Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (7 domains)

CATH v4.4 (5 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)