SAXSdb — 5acm

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

MCG

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–110	Fragment：IG LAMBDA CHAIN V-II REGION MGC	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–110	Fragment：IG LAMBDA CHAIN V-II REGION MGC	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

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 5ACM	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
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 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 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

7 other PDB entries and 7 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

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	5acm
Deposition date deposition_date	2015-08-17
Structure title title	Mcg immunoglobulin variable domain with methylene blue
Keywords keywords	IMMUNE SYSTEM, MCG, IMMUNOGLOBULIN VARIABLE DOMAIN, METHYLENE BLUE; 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	18.56 Å
Radius of gyration Rg (electron density) rg_electron	17.52 Å
Forward intensity I(0) i0	11534100.00
Molecular weight molecular_weight	23600.0 kDa
Excluded volume excluded_volume	28707 Å³
Envelope volume envelope_volume	33218 Å³
Hydration-shell volume shell_volume	16217 Å³
Envelope diameter envelope_diameter	57.5 Å
Shell Rg shell_rg	23.12 Å
Envelope Rg envelope_rg	17.57 Å
Shape Rg shape_rg	17.45 Å
Total Rg total_rg	18.51 Å
Total atoms total_atoms	1652
Residues n_residues	218
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	71.8 Å
Rg (real space) rg_real	18.47 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.1530e+07
I(0) uncertainty (real space) i0_real_error	1.4590e+05
Rg (reciprocal space) rg_reciprocal	18.49 Å
I(0) (reciprocal space) i0_reciprocal	11530000.0000
Solution quality estimate total_estimate	0.7351
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.6 Å
Skewness Skewness skewness	0.154
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.4300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3234000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.559; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	MCG
Molecular weight formula_weight	11565.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1873

GQSALTQPPSASGSLGQSVTISCTGTSSDVGGYNYVSWYQQHAGKAPKVIIYEVNKRPSGVPDRFSGSKSGNTASLTVSGLQAEDEADYYCSSYEGSDNFVFGTGTKVTVL

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	3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM
Molecular weight formula_weight	284.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	208

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5acma_
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	d5acmb_
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

CATH v4.4 (2 domains)

Domain ID domain_id	5acmA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5acmB00
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	39.220 Å
Unit-cell length b length_b	31.080 Å
Unit-cell length c length_c	73.630 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.050 Å
Low-resolution limit resolution_low	39.220 Å
R factor r_factor	0.1109
R_work r_work	0.1103
R_free r_free	0.1223

fit	/app/data/saxs_computation/ac/5acm/5acm.fit
pddf	/app/data/pr_computation/ac/5acm/5acm.pr.out
profile	/app/data/saxs_computation/ac/5acm/5acm.dat

Mcg immunoglobulin variable domain with methylene blue

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

MCG

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