1c5d

THE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR

Method: X-RAY DIFFRACTION D_max: 113.7 Å Quality: GOOD

▼

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

No usable UniProt protein identity is available for this entry.

七张关系表仍保留该条目的 assembly 与组成信息，但缺少统一蛋白身份时，不能可靠建立跨 PDB 的同蛋白Chain接。

Assembly Composition of the Current Entry

Assembly	Oligomeric State	实体与Construct证据	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer 蛋白 4 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: tetrameric	Entity 1：MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR × 2 Entity 2：MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR × 2 缺少 UniProt 身份时不显示参考序列区间	Entity 1Fragment：FAB FRAGMENT, HEAVY CHAIN Entity 2Fragment：FAB FRAGMENT, LIGHT CHAIN	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；289 K；12 MG/ML FAB192, 18% W/V PEG6000, 150 MM NACL, 100 MM BIS-TRIS/HCL, PH 7.5, 2 MM EDTA, AT 16 DEG. C, temperature 289K	Resolution 2.40 Å R-free 0.304
2	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR × 1 Entity 2：MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR × 1 缺少 UniProt 身份时不显示参考序列区间	Entity 1Fragment：FAB FRAGMENT, HEAVY CHAIN Entity 2Fragment：FAB FRAGMENT, LIGHT CHAIN	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；289 K；12 MG/ML FAB192, 18% W/V PEG6000, 150 MM NACL, 100 MM BIS-TRIS/HCL, PH 7.5, 2 MM EDTA, AT 16 DEG. C, temperature 289K	Resolution 2.40 Å R-free 0.304
3	Protein heterocomplex Heteromer 蛋白 2 / DNA 0 / RNA 0 / 其他Polymer 0 PDB declaration: dimeric	Entity 1：MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR × 1 Entity 2：MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR × 1 缺少 UniProt 身份时不显示参考序列区间	Entity 1Fragment：FAB FRAGMENT, HEAVY CHAIN Entity 2Fragment：FAB FRAGMENT, LIGHT CHAIN	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；289 K；12 MG/ML FAB192, 18% W/V PEG6000, 150 MM NACL, 100 MM BIS-TRIS/HCL, PH 7.5, 2 MM EDTA, AT 16 DEG. C, temperature 289K	Resolution 2.40 Å R-free 0.304

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1c5d
Deposition date deposition_date	1999-11-17
Structure title title	THE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
Keywords keywords	IMMUNOGLOBULIN, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	34.73 Å
Radius of gyration Rg (electron density) rg_electron	34.08 Å
Forward intensity I(0) i0	136833000.00
Molecular weight molecular_weight	92544.0 kDa
Excluded volume excluded_volume	115250 Å³
Envelope volume envelope_volume	150570 Å³
Hydration-shell volume shell_volume	37723 Å³
Envelope diameter envelope_diameter	113.3 Å
Shell Rg shell_rg	39.99 Å
Envelope Rg envelope_rg	33.27 Å
Shape Rg shape_rg	34.05 Å
Total Rg total_rg	34.62 Å
Total atoms total_atoms	6506
Residues n_residues	855
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

▼

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

Maximum dimension Dmax dmax	113.7 Å
Rg (real space) rg_real	34.75 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.3680e+08
I(0) uncertainty (real space) i0_real_error	2.0690e+06
Rg (reciprocal space) rg_reciprocal	34.74 Å
I(0) (reciprocal space) i0_reciprocal	136800000.0000
Solution quality estimate total_estimate	0.8942
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	39.5 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.558
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14090000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.935; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.838

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
Molecular weight formula_weight	23361.0 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,A
Atom count atom_count	6715

DIQMTQSPPSLSASLGDKVTITCQASQDINKYIAWYQQKPGKAPRQLIRYTSILVLGTPSRFSGSGSGRDFSFSISNVASEDIASYYCLQYGNLYTFGAGTKLEIKRADAAPTVSIFPPSTEQLATGGASVVCLMNNFYPRDISVKWKIDGTERRDGVLDSVTDQDSKDSTYSMSSTLSLTKADYESHNLYTCEVVHKTSSSPVVKSFNRNEC

Entity 2 Entity 2 polymer

Description description	MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR
Molecular weight formula_weight	23053.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,B

EVKLLESGPGLVQPSQTLSLTCTVSGFPLTTNGVSWVRQPPGKGLEWIAAISSGGSPYYNSALKSRLSINRDTSKSQVFLKMNSLQTEDTAIYFCTREDGWNYFDYWGPGTMVTVSSAQTTAPSVYPLAPGCGDTTSSTVTLGCLVKGYFPEPVTVTWNSGALSSDVHTFPAVLQSGLYTLTSSVTSSTWPSQTVTCNVAHPASSTKVDKKLERR

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	209

▼

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1c5da1
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	d1c5da2
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	d1c5db1
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	d1c5db2
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	d1c5dh1
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	d1c5dh2
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	d1c5dl1
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	d1c5dl2
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 (8 domains)

Domain ID domain_id	1c5dA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1c5dL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	79.710 Å
Unit-cell length b length_b	110.080 Å
Unit-cell length c length_c	199.520 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	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.3040

fit	/app/data/saxs_computation/c5/1c5d/1c5d.fit
pddf	/app/data/pr_computation/c5/1c5d/1c5d.pr.out
profile	/app/data/saxs_computation/c5/1c5d/1c5d.dat

THE CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF A RAT MONOCLONAL ANTIBODY AGAINST THE MAIN IMMUNOGENIC REGION OF THE HUMAN MUSCLE ACETYLCHOLINE RECEPTOR

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

Assembly Composition of the Current Entry

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)