4unt

Induced monomer of the Mcg variable domain

Method: X-RAY DIFFRACTION D_max: 92.8 Å Quality: GOOD

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

IG LAMBDA CHAIN V-II REGION MGC

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 1–110 Chain B； UniProt 1–110 Chain C； UniProt 1–110 Chain D； UniProt 1–110 Chain E； UniProt 1–110 Chain F； UniProt 1–110 Chain G； UniProt 1–110 Chain H； UniProt 1–110	Fragment：LIGHT-CHAIN VARIABLE DOMAIN, RESIDUES 1-110 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

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 4UNT	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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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
2MCG THREE-DIMENSIONAL STRUCTURE OF A LIGHT CHAIN DIMER CRYSTALLIZED IN WATER. CONFORMATIONAL FLEXIBILITY OF A MOLECULE IN TWO CRYSTAL FORMS Deposited 1989-05-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain 1 21–235（215 aa） Chain 2 21–235（215 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
4UNU MCG - a dimer of lambda variable domains 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 × 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 oligomeric state 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	LV206_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–111； UniProt 1–110 Author chain B； PDBConstruct 2–111； UniProt 1–110 Author chain C； PDBConstruct 2–111； UniProt 1–110 Author chain D； PDBConstruct 2–111； UniProt 1–110 Author chain E； PDBConstruct 2–111； UniProt 1–110 Author chain F； PDBConstruct 2–111； UniProt 1–110 Author chain G； PDBConstruct 2–111； UniProt 1–110 Author chain H； PDBConstruct 2–111； UniProt 1–110

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4unt
Deposition date deposition_date	2014-05-30
Structure title title	Induced monomer of the Mcg variable domain
Keywords keywords	IMMUNE SYSTEM, BENCE-JONES, LIGHT CHAINS, IMMUNOGLOBULIN, AMYLOID; 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	30.69 Å
Radius of gyration Rg (electron density) rg_electron	30.30 Å
Forward intensity I(0) i0	150560000.00
Molecular weight molecular_weight	89593.0 kDa
Excluded volume excluded_volume	108650 Å³
Envelope volume envelope_volume	142750 Å³
Hydration-shell volume shell_volume	39017 Å³
Envelope diameter envelope_diameter	101.4 Å
Shell Rg shell_rg	37.72 Å
Envelope Rg envelope_rg	29.65 Å
Shape Rg shape_rg	30.25 Å
Total Rg total_rg	31.05 Å
Total atoms total_atoms	6270
Residues n_residues	864
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	92.8 Å
Rg (real space) rg_real	30.49 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	1.5060e+08
I(0) uncertainty (real space) i0_real_error	2.0280e+06
Rg (reciprocal space) rg_reciprocal	30.58 Å
I(0) (reciprocal space) i0_reciprocal	150600000.0000
Solution quality estimate total_estimate	0.8999
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	42.8 Å
Skewness Skewness skewness	0.084
Kurtosis Kurtosis kurtosis	-0.478
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	14350000.0000
Real-space data points n_real_points	53
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: 0.989; Smooth: 0.902

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	IG LAMBDA CHAIN V-II REGION MGC
Molecular weight formula_weight	11437.3 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	6328

GQSALTQPPSASGSLGQSVTISCTGTSSDVGGYNYVSWEQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNAVEGTGTKVTVL

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	57

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4unta_
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	d4untb_
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	d4untc_
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	d4untd_
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	d4unte_
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	d4untf_
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	d4untg_
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	d4unth_
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)

CATH v4.4 (8 domains)

Domain ID domain_id	4untA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4untH00
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 (1)

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Unit-cell length a length_a	103.130 Å
Unit-cell length b length_b	90.350 Å
Unit-cell length c length_c	99.170 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	63.880 Å
R factor r_factor	0.2456
R_work r_work	0.2433
R_free r_free	0.2893

fit	/app/data/saxs_computation/un/4unt/4unt.fit
pddf	/app/data/pr_computation/un/4unt/4unt.pr.out
profile	/app/data/saxs_computation/un/4unt/4unt.dat