SAXSdb — 1kc5

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

PC287 Immunoglobulin

OrganismNot specified

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain L； UniProt 42–239	Fragment：light chain	PC287 Immunoglobulin × 1 （P01869） PS1 peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；300 K；20% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.50 Å R-free 0.270

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	Q8VC55
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain L； PDBConstruct 22–214； UniProt 42–239

PC287 Immunoglobulin

OrganismNot specified

UniProt P01869

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain H； UniProt 1–101	Fragment：heavy chain	PC287 Immunoglobulin × 1 （Q8VC55） PS1 peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；300 K；20% PEG 8K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.50 Å R-free 0.270

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 1KC5	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
15C8 CATALYTIC ANTIBODY 5C8, FREE FAB Deposited 1998-03-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–217（216 aa） Fragment：FAB	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.50 Å R-free 0.251
1ACY CRYSTAL STRUCTURE OF THE PRINCIPAL NEUTRALIZING SITE OF HIV-1 Deposited 1994-02-10	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–100（100 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1AE6 IGG-FAB FRAGMENT OF MOUSE MONOCLONAL ANTIBODY CTM01 Deposited 1997-03-06	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–98（98 aa） Fragment：FAB FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；20-25% PEG4000, BUFFERED AT PH 5.6 WITH 20MM BIS-TRIS.	Resolution 3.00 Å R-free 0.311
1CIC IDIOTOPE-ANTI-IDIOTOPE FAB-FAB COMPLEX; D1.3-E225 Deposited 1999-03-31	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–218（218 aa） Fragment：FAB IMMUNOGLOBULIN FRAGMENT	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.9；12% PEG 800, 75 MILLIMOLAR SODIUM ACETATE PH 4.85 10MGM/ML PROTEIN CONCENTRATION , pH 4.9	Resolution 2.50 Å
1CL7 ANTI HIV1 PROTEASE FAB Deposited 1999-05-06	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 133–214（82 aa） Fragment：FAB	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 3.00 Å R-free 0.280
1F11 F124 FAB FRAGMENT FROM A MONOCLONAL ANTI-PRES2 ANTIBODY Deposited 2000-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–102（101 aa） Fragment：FAB FRAGMENT (UNP Q65ZR6 residues 18-134, P01869 residues 2-102)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；PEG 400, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.00 Å R-free 0.271
1F11 F124 FAB FRAGMENT FROM A MONOCLONAL ANTI-PRES2 ANTIBODY Deposited 2000-05-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 2–102（101 aa） Fragment：FAB FRAGMENT (UNP Q65ZR6 residues 18-134, P01869 residues 2-102)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；290 K；PEG 400, sodium acetate, ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.00 Å R-free 0.271
1JHK Crystal structure of the anti-estradiol antibody 57-2 Deposited 2001-06-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 12–229（218 aa） Fragment：residues 1-215	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；277 K；PEG4000, PEG8000, Tris-HCl, pH 9.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.51 Å R-free 0.262
1KCR CRYSTAL STRUCTURE OF ANTIBODY PC283 IN COMPLEX WITH PS1 PEPTIDE Deposited 2001-11-11	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 1–102（102 aa） Fragment：heavy chain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；300 K；18% PEG 3K, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.90 Å R-free 0.277
1L7T Crystal Structure Analysis of the anti-testosterone Fab fragment Deposited 2002-03-17	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–103（103 aa） Fragment：fab77 fragment	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；peg3350, MES, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.275
1ORS X-ray structure of the KvAP potassium channel voltage sensor in complex with an Fab Deposited 2003-03-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–103（103 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG4000, Hepes, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.90 Å R-free 0.251
1RUQ Crystal Structure (H) of u.v.-irradiated Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set collected in house. Deposited 2003-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa） Fragment：fab	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M imidazole, pH 8.0, 0.2 M zinc acetate, 5-7% (v/v) isopropanol, 20% (w/v) PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.86 Å R-free 0.256
1RUR Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set collected at SSRL beamline 9-1. Deposited 2003-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–99（99 aa） Fragment：fab	Not recorded	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M imidazole, pH 8.0, 0.2 M zinc acetate, 5-7% (v/v) isopropanol, 20% (w/v) PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 1.50 Å R-free 0.238
1S5I Fab (LNKB-2) of monoclonal antibody to Human Interleukin-2, crystal structure Deposited 2004-01-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 1–102（102 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；300 K；PEG-8000, ZnAc, NaN3, Na(CH3)2AsO4, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K	Resolution 2.70 Å R-free 0.275
25C8 CATALYTIC ANTIBODY 5C8, FAB-HAPTEN COMPLEX Deposited 1998-03-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–217（216 aa） Fragment：FAB	Not recorded	GEP N-METHYL-N-(PARA-GLUTARAMIDOPHENYL-ETHYL)-PIPERIDINIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；pH 5.5	Resolution 2.00 Å R-free 0.292

14 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGH1M_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain H； PDBConstruct 117–217； UniProt 1–101

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	1kc5
Deposition date deposition_date	2001-11-07
Structure title title	CRYSTAL STRUCTURE OF ANTIBODY PC287 IN COMPLEX WITH PS1 PEPTIDE
Keywords keywords	ANTIBODY, PEPTIDE ANTIGEN, COMPLEX (ANTIBODY-PEPTIDE), 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	25.95 Å
Radius of gyration Rg (electron density) rg_electron	24.92 Å
Forward intensity I(0) i0	38816100.00
Molecular weight molecular_weight	47453.0 kDa
Excluded volume excluded_volume	58984 Å³
Envelope volume envelope_volume	73317 Å³
Hydration-shell volume shell_volume	24761 Å³
Envelope diameter envelope_diameter	83.4 Å
Shell Rg shell_rg	32.04 Å
Envelope Rg envelope_rg	24.52 Å
Shape Rg shape_rg	24.91 Å
Total Rg total_rg	25.77 Å
Total atoms total_atoms	3341
Residues n_residues	439
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	80.5 Å
Rg (real space) rg_real	25.94 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.8820e+07
I(0) uncertainty (real space) i0_real_error	5.0040e+05
Rg (reciprocal space) rg_reciprocal	25.94 Å
I(0) (reciprocal space) i0_reciprocal	38820000.0000
Solution quality estimate total_estimate	0.9126
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.7 Å
Skewness Skewness skewness	0.265
Kurtosis Kurtosis kurtosis	-0.591
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8165000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PC287 Immunoglobulin
Molecular weight formula_weight	23478.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L
Atom count atom_count	3517

DIVLTQSPKSMSMSVGEKVTLSCKASENVDTYVSWYQQRPEQPPALLIYGASNRYTGVPDRFTGSGSATDFTLTISSVQAEDLADYHCGQSYSYPLTFGGGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVANSWTAQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPVVKSFNRNEC

Entity 2 Entity 2 polymer

Description description	PC287 Immunoglobulin
Molecular weight formula_weight	23206.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVKLQQSGPGLVKPSQSLSLTCTVTGYSITSDYAWNWIRQFPGNKLEWMAYISYSGSTTYNPSLKSRISITRDTSKNQFFLQLNSVTTEDTAIYYCARGGTGFDYWGAGTTLTVSAAATTPPSVYPLAPGSATAAASMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSDLYTLSSSVTVPSSPWPSETVTCNVAHPASSTKVDKKIVPRD

Entity 3 Entity 3 polymer

Description description	PS1 peptide
Molecular weight formula_weight	1584.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

HQLDPAFGANSTNPD

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	176

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1kc5h1
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	d1kc5h2
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	d1kc5l1
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	d1kc5l2
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 (4 domains)

Domain ID domain_id	1kc5H01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kc5H02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kc5L01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1kc5L02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (2)

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Unit-cell length a length_a	73.590 Å
Unit-cell length b length_b	71.588 Å
Unit-cell length c length_c	87.677 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.1950
R_free r_free	0.2700

fit	/app/data/saxs_computation/kc/1kc5/1kc5.fit
pddf	/app/data/pr_computation/kc/1kc5/1kc5.pr.out
profile	/app/data/saxs_computation/kc/1kc5/1kc5.dat

CRYSTAL STRUCTURE OF ANTIBODY PC287 IN COMPLEX WITH PS1 PEPTIDE

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

PC287 Immunoglobulin

State in the Current Structure

Other States of the Same Protein in the Database

PC287 Immunoglobulin

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)