SAXSdb — 2mcg

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

IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)

Homo sapiens

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain 1； UniProt 21–235 Chain 2； UniProt 21–235	Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.00 Å

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 2MCG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A8J IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER (MCG) COMPLEX WITH ASPARTAME Deposited 1998-03-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain H 21–235（215 aa） Chain L 21–235（215 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	PME N-L-ALPHA-ASPARTYL L-PHENYLALANINE 1-METHYL ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；PROTEIN WAS CRYSTALLIZED IN FRESH 1.9M AMMONIUM SULFATE BUFFERED AT PH 6.2 WITH PHOSPHATE AND THE MOTHER LIQUOR WAS SATURATED WITH ASPARTAME.	Resolution 2.70 Å R-free 0.380
1DCL MCG, A LAMBDA V TYPE LIGHT-CHAIN DIMER (BENCE-JONES PROTEIN), CRYSTALLIZED FROM AMMONIUM SULFATE Deposited 1995-10-16	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 21–235（215 aa） Chain B 21–235（215 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions CRYSTALLIZED FROM AMMONIUM SULFATE	Resolution 2.30 Å
4UNT Induced monomer of the Mcg variable domain Deposited 2014-05-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain B 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain C 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain D 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain E 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain F 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain G 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain H 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110	Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES Mutation：YES	SO4 SULFATE ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.5M LICL, 1.65M (NH4)2SO4, pH 8	Resolution 2.70 Å R-free 0.289
4UNU MCG - a dimer of lambda variable domains Deposited 2014-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 Chain B 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110	Not recorded	15P POLYETHYLENE GLYCOL (N=34) × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；2M NACL, 2M (NH4)2SO4, pH 8	Resolution 0.95 Å R-free 0.130
4UNV Covalent dimer of lambda variable domains Deposited 2014-05-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–110（110 aa） Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110	Mutation：YES	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；0.1M CH3COONA PH4.6, 2M (NH4)2SO4	Resolution 1.60 Å R-free 0.258
5ACL Mcg immunoglobulin variable domain with sulfasalazine Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa） Fragment：IG LAMBDA CHAIN V-II REGION MGC	Not recorded	SAS 2-HYDROXY-(5-([4-(2-PYRIDINYLAMINO)SULFONYL]PHENYL)AZO)BENZOIC ACID × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2 M TRI-POTASSIUM CITRATE, 2.2 M (NH4)2SO4, 0.5 M SULFASALAZINE, pH 8.5	Resolution 1.49 Å R-free 0.187
5ACM Mcg immunoglobulin variable domain with methylene blue Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–110（110 aa） Fragment：IG LAMBDA CHAIN V-II REGION MGC	Not recorded	MBT 3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5	Resolution 1.05 Å R-free 0.122
5ACM Mcg immunoglobulin variable domain with methylene blue Deposited 2015-08-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–110（110 aa） Fragment：IG LAMBDA CHAIN V-II REGION MGC	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.2 M NH4CL, 2.2 M (NH4)2SO4, 0.5 M METHYLENE BLUE, pH 8.5	Resolution 1.05 Å R-free 0.122

7 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LV2F_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 2–216； UniProt 21–235 Author chain 2； PDBConstruct 2–216； UniProt 21–235

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	2mcg
Deposition date deposition_date	1989-05-09
Structure title title	THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS
Keywords keywords	IMMUNOGLOBULIN; IMMUNOGLOBULIN
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	24.71 Å
Radius of gyration Rg (electron density) rg_electron	23.67 Å
Forward intensity I(0) i0	37111500.00
Molecular weight molecular_weight	45624.0 kDa
Excluded volume excluded_volume	56445 Å³
Envelope volume envelope_volume	69402 Å³
Hydration-shell volume shell_volume	24735 Å³
Envelope diameter envelope_diameter	79.5 Å
Shell Rg shell_rg	30.40 Å
Envelope Rg envelope_rg	23.49 Å
Shape Rg shape_rg	23.65 Å
Total Rg total_rg	24.49 Å
Total atoms total_atoms	3212
Residues n_residues	430
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	82.8 Å
Rg (real space) rg_real	24.68 Å
Rg uncertainty (real space) rg_real_error	0.58 Å
I(0) (real space) i0_real	3.7110e+07
I(0) uncertainty (real space) i0_real_error	5.1030e+05
Rg (reciprocal space) rg_reciprocal	24.69 Å
I(0) (reciprocal space) i0_reciprocal	37110000.0000
Solution quality estimate total_estimate	0.8906
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.295
Kurtosis Kurtosis kurtosis	-0.428
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4870000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2mcg11
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	d2mcg12
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	d2mcg21
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	d2mcg22
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	2mcg101
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2mcg102
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2mcg201
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2mcg202
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 (19)

;Three-dimensional structure of a light chain dimer crystallized in water. Conformational flexibility of a molecule in two crystal forms. ;

J.Mol.Biol. (1989)

PMID: 2515285 · DOI: 10.1016/0022-2836(89)90135-6 PRIMARY

The Binding of Opioid Peptides to the Mcg Light Chain Dimer. Flexible Keys and Adjustable Locks

Mol.Immunol. (1987)

Three-Dimensional Structure of the Orthorhombic Form of the Mcg Bence-Jones Dimer

Progress in Immunology V (1983)

Small-Angle Neutron Scattering Study of Bence-Jones Protein Mcg. Comparison of Structures in Solution and in Crystal

Biochemistry (1982)

Marked Structural Differences of the Mcg Bence-Jones Dimer in Two Crystal Systems

Biochemistry (1980)

Crystal Properties as Indicators of Conformational Changes During Ligand Binding or Interconversion of Mcg Light Chain Isomers

Biochemistry (1978)

Interconversion of Conformational Isomers of Light Chains in the Mcg Immunoglobulins

Biochemistry (1978)

The Antibody Combining Site

Sci.Am. (1977)

Implications of Conformational Isomerism and Rotational Allomerism to the Binding of Small Molecules by the Mcg Bence-Jones Dimer

Antibodies in Human Diagnosis and Therapy (1977)

Conformational Isomerism,Rotational Allomerism, and Divergent Evolution in Immunoglobulin Light Chains

FED.PROC. (1976)

Rotational Allomerism and Divergent Evolution of Domains in Immunoglobulin Light Chains

Biochemistry (1975)

Binding of 2,4-Dinitrophenyl Compounds and Other Small Molecules to a Crystalline Lambda-Type Bence-Jones Dimer

Biochemistry (1974)

Structure and Binding Properties of a Lambda-Type Bence-Jones Dimer

Progress in Immunology II (1974)

Primary Structure of the Mcg Lambda Chain

Biochemistry (1974)

Preparation and Properties of a Bence-Jones Dimer with Mercury Inserted Into the Interchain Disulfide Bond

Biochemistry (1973)

Structure of a Lambda-Type Bence-Jones Protein at 3.5-Angstroms Resolution

Biochemistry (1973)

Structural Features of Immunoglobulin Light Chains

Prog.Mol.Subcell.Biol. (1973)

Structure of a Lambda-Type Bence-Jones Protein at 6-Angstroms Resolution

Biochemistry (1972)

Crystallographic Studies of an Igg Immunoglobulin and the Bence-Jones Protein from One Patient

Cold Spring Harbor Symp.Quant.Biol. (1972)

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Unit-cell length a length_a	72.300 Å
Unit-cell length b length_b	72.300 Å
Unit-cell length c length_c	185.900 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1870
R_work r_work	—
R_free r_free	—

Description description	IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)
Molecular weight formula_weight	22833.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2
Atom count atom_count	3530

THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS

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

IMMUNOGLOBULIN LAMBDA DIMER MCG (LIGHT CHAIN)

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (19)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

fit	/app/data/saxs_computation/mc/2mcg/2mcg.fit
pddf	/app/data/pr_computation/mc/2mcg/2mcg.pr.out
profile	/app/data/saxs_computation/mc/2mcg/2mcg.dat