SAXSdb — 5gxb

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

Lactose permease

Escherichia coli (strain K12)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–417	Not recorded	nanobody × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；100mM MES pH 6.0, 100mM (NH4)2C4H4O6, 43% PEG 400	Resolution 3.30 Å R-free 0.346

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 5GXB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PV6 Crystal structure of lactose permease Deposited 2003-06-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.337
1PV6 Crystal structure of lactose permease Deposited 2003-06-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.50 Å R-free 0.337
1PV7 Crystal structure of lactose permease with TDG Deposited 2003-06-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.296
1PV7 Crystal structure of lactose permease with TDG Deposited 2003-06-26	Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Mutation：C154G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 400, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.60 Å R-free 0.296
2CFP Sugar Free Lactose Permease at acidic pH Deposited 2006-02-22	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 1–417（417 aa）	Mutation：YES	HG MERCURY (II) ION × 5	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.30 Å R-free 0.328
2CFQ Sugar Free Lactose Permease at neutral pH Deposited 2006-02-22	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 1–417（417 aa）	Mutation：YES	HG MERCURY (II) ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.50	Resolution 2.95 Å R-free 0.298
2V8N Wild-type Structure of Lactose Permease Deposited 2007-08-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–417（417 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.60 Å R-free 0.333
2V8N Wild-type Structure of Lactose Permease Deposited 2007-08-09	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–417（417 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 3.60 Å R-free 0.333
2Y5Y Crystal structure of LacY in complex with an affinity inactivator Deposited 2011-01-19	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 1–417（417 aa） Chain B 1–417（417 aa）	Mutation：YES Mutation：YES	BA BARIUM ION × 2 TGA 2-sulfanylethyl beta-D-galactopyranoside × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PH 6	Resolution 3.38 Å R-free 0.303
4ZYR Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG) Deposited 2015-05-22	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 1–417（417 aa）	Mutation：G46W, G262W	9PG 4-nitrophenyl alpha-D-galactopyranoside × 1 BNG nonyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；1.0 M NaCl 0.05 M Tris (pH8.0) 26% PEG 600	Resolution 3.31 Å R-free 0.278
4ZYR Crystal structure of E. coli Lactose permease G46W/G262W bound to p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG) Deposited 2015-05-22	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 1–417（417 aa）	Mutation：G46W, G262W	9PG 4-nitrophenyl alpha-D-galactopyranoside × 1 BNG nonyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295 K；1.0 M NaCl 0.05 M Tris (pH8.0) 26% PEG 600	Resolution 3.31 Å R-free 0.278
6C9W Crystal Structure of a ligand bound LacY/Nanobody Complex Deposited 2018-01-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–417（417 aa） Fragment：Full	Mutation：G46W, G262W	9PG 4-nitrophenyl alpha-D-galactopyranoside × 1 BNG nonyl beta-D-glucopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；295 K；0.1 M MgCl2, 28% PEG1000, 0.1 M Tris-HCl, pH 8.5	Resolution 3.00 Å R-free 0.295
8Y9Y Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+1C) Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 315–334（20 aa）	Mutation：T1M,R2A,L3K,A4K,G5T,C53A	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.29 Å
8YA0 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 316–332（17 aa）	Mutation：R2A, L3K, A4K, G5T, C14T, F17L	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
8YA2 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+20C) Deposited 2024-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 315–334（20 aa）	Mutation：T1M,R2A,L3K,A4K,G5T,E45C,C53A	MG MAGNESIUM ION × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
8YA3 Structure of the SecA-SecY complex with the substrate FtsQ-LacY(+7C) treated with DTT Deposited 2024-02-07	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 315–334（20 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.27 Å
9XOU CryoEM structure of LacY with Trimbody Deposited 2025-11-15	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain G 1–417（417 aa） Chain H 1–417（417 aa） Chain I 1–417（417 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å

13 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LACY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–417； UniProt 1–417

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	5gxb
Deposition date deposition_date	2016-09-16
Structure title title	crystal structure of a LacY/Nanobody complex
Keywords keywords	transporter, TRANSPORT PROTEIN; TRANSPORT PROTEIN
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	27.20 Å
Radius of gyration Rg (electron density) rg_electron	26.46 Å
Forward intensity I(0) i0	46192800.00
Molecular weight molecular_weight	58231.0 kDa
Excluded volume excluded_volume	74975 Å³
Envelope volume envelope_volume	87947 Å³
Hydration-shell volume shell_volume	28935 Å³
Envelope diameter envelope_diameter	99.7 Å
Shell Rg shell_rg	32.57 Å
Envelope Rg envelope_rg	26.65 Å
Shape Rg shape_rg	26.43 Å
Total Rg total_rg	27.24 Å
Total atoms total_atoms	4121
Residues n_residues	519
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	97.2 Å
Rg (real space) rg_real	27.38 Å
Rg uncertainty (real space) rg_real_error	0.92 Å
I(0) (real space) i0_real	4.6190e+07
I(0) uncertainty (real space) i0_real_error	8.0640e+05
Rg (reciprocal space) rg_reciprocal	27.33 Å
I(0) (reciprocal space) i0_reciprocal	46190000.0000
Solution quality estimate total_estimate	0.8437
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.535
Kurtosis Kurtosis kurtosis	-0.103
Angular range angular_range	— – 0.2900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9509000.0000
Real-space data points n_real_points	59
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.710; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.875; Smooth: 0.957

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Lactose permease
Molecular weight formula_weight	47618.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4121

MYYLKNTNFWMFGLFFFFYFFIMGAYFPFFPIWLHDINHISKSDTWIIFAAISLFSLLFQPLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGSGCALILAVLLFFAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQFANFFTSFFATGEQGTRVFWYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRIIGSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIFMSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLSGPGPLSLLRRQVNEVAHHHHHH

来源 Source

来源生物 organism	Escherichia coli (strain K12)
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	nanobody
Molecular weight formula_weight	15690.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MQVQLVESGGRLVQAGDSLRLSCAASGRTFTTYLMGWFRQAPGKEREFVAAIRWSGGSTYYADSVKGRFTISRDNAKNTVYLQMNSLKLEDTAVYYCAAAARPSYSGDYGYTEALRYDYWGQGTQVTVSSHHHHHHEPEA

来源 Source

来源生物 organism	Vicugna pacos
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5gxbA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	20 — MFS general substrate transporter like domains

Domain ID domain_id	5gxbA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	20 — MFS general substrate transporter like domains

Domain ID domain_id	5gxbB00
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	96.543 Å
Unit-cell length b length_b	96.543 Å
Unit-cell length c length_c	145.025 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	8

Space group space_group	P 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	48.342 Å
R factor r_factor	0.3400
R_work r_work	0.3397
R_free r_free	0.3465

fit	/app/data/saxs_computation/gx/5gxb/5gxb.fit
pddf	/app/data/pr_computation/gx/5gxb/5gxb.pr.out
profile	/app/data/saxs_computation/gx/5gxb/5gxb.dat

crystal structure of a LacY/Nanobody complex

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

Lactose permease

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)