SAXSdb — 8wfi

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

Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1

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 46–614	Not recorded	GLY GLYCINE × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.58 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 8WFI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6ZBV Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor and sybody Sb_GlyT1#7 Deposited 2020-06-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 91–239（149 aa） Chain A 257–684（428 aa）	Not recorded	QET [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；292.75 K；0.1M ADA pH 7, 13-25% PEG600, 4-14% v/v-1,3-Butanediol	Resolution 3.40 Å R-free 0.259
6ZPL Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions. Deposited 2020-07-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 92–684（593 aa） Chain B 92–684（593 aa）	Mutation：;L153A, S297A, I368A, C633A. N-terminal deletion of residues 1-91 and residues 9-281 of Lichenase (PDB ID 2CIT) have been fused at the N-terminal. C- terminal deletion of residues 685-706 as well as a deletion in the extracellular loop 2 (EL2) between residues 240-256. ; Mutation：;L153A, S297A, I368A, C633A. N-terminal deletion of residues 1-91 and residues 9-281 of Lichenase (PDB ID 2CIT) have been fused at the N-terminal. C- terminal deletion of residues 685-706 as well as a deletion in the extracellular loop 2 (EL2) between residues 240-256. ;	QET [5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7；292.75 K；Crystals appeared in 3-10 days in 0.1 M ADA pH 7, 13-25% PEG600, 4-14% v/v, 1,3-Butanediol with the longest dimension of 2-5 um.	Resolution 3.94 Å R-free 0.291
8WFJ human glycine transporter 1 in complex with ALX-5407 in inward facing conformation Deposited 2023-09-19	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–652（652 aa）	Not recorded	W5F ALX5407 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.35 Å
8WFK human glycine transporter 1 in complex with SSR504734 in outward facing conformation Deposited 2023-09-19	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–652（652 aa）	Not recorded	W5O SSR504734 × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.22 Å
8WFL human glycine transporter 1 in complex with PF-03463275 in outward facing conformation Deposited 2023-09-19	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–652（652 aa）	Not recorded	W5X PF-3463275 × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
9J8B Human Glycine Transporter 1 in the Apo State with an Inward-Facing Conformation Deposited 2024-08-21	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–652（652 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
9J8C Human Glycine Transporter 1 in the Sarcosine-Bound State with an Occluded Conformation Deposited 2024-08-21	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–652（652 aa）	Not recorded	SAR SARCOSINE × 1 CLR CHOLESTEROL × 3 CL CHLORIDE ION × 1 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9J8D Human Glycine Transporter 1 in the Iclepertin-Bound State with an Inward-Facing Conformation Deposited 2024-08-21	Different construct Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–652（652 aa）	Not recorded	A1EBX Iclepertin × 1 CL CHLORIDE ION × 1 CLR CHOLESTEROL × 3 NA SODIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

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

View Construct and Data Evidence

UniProt name	SC6A9_HUMAN
Isoform	P48067-3
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–569； UniProt 46–614

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	8wfi
Deposition date deposition_date	2023-09-19
Structure title title	human glycine transporter 1 in complex with glycine in occluded conformation
Keywords keywords	GlyT1, glycine, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	25.56 Å
Radius of gyration Rg (electron density) rg_electron	24.33 Å
Forward intensity I(0) i0	51003800.00
Molecular weight molecular_weight	61063.0 kDa
Excluded volume excluded_volume	78593 Å³
Envelope volume envelope_volume	93105 Å³
Hydration-shell volume shell_volume	31366 Å³
Envelope diameter envelope_diameter	86.8 Å
Shell Rg shell_rg	32.18 Å
Envelope Rg envelope_rg	24.59 Å
Shape Rg shape_rg	24.34 Å
Total Rg total_rg	25.23 Å
Total atoms total_atoms	4310
Residues n_residues	542
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	83.8 Å
Rg (real space) rg_real	25.55 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	5.1000e+07
I(0) uncertainty (real space) i0_real_error	7.0490e+05
Rg (reciprocal space) rg_reciprocal	25.55 Å
I(0) (reciprocal space) i0_reciprocal	51000000.0000
Solution quality estimate total_estimate	0.7233
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.7 Å
Skewness Skewness skewness	0.380
Kurtosis Kurtosis kurtosis	-0.218
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9856000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.843; Stabil: 1.000; Sysdev: 0.315; Positv: 1.000; Valcen: 1.000; Smooth: 0.926

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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	Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1
Molecular weight formula_weight	63769.5 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	4347

RGNWGNQIEFVLTSVGYAVGLGNVWRFPYLCYRNAGGAFMFPYFIMLIFCGIPLFFMELSFGQFASQGCLGVWRISPMFKGVGYGMMVVSTYIGIYYNVVICIAFYYFFSSMTHVLPWAYCNNPWNTHDCAGVLDASNLTNGSRPAALPSNLSHLLNHSLQRTSPSEEYWRLYVLKLSDDIGNFGEVRLPLLGCLGVSWLVVFLCLIRGVKSSGKVVYFTATFPYVVLTILFVRGVTLEGAFDGIMYYLTPQWDKILAAKVWGDAASQIFYSLGCAWGGLITMASYNKFHNNCYRDSVIISITNCATSVYAGFVIFSILGFMANHLGVDVSRVADHGPGLAFVAYPEALTLLPISPLWSLLFFFMLILLGLGTQFCLLETLVTAIVDEVGNEWILQKKTYVTLGVAVAGFLLGIPLTSQAGIYWLLLMDNYAASFSLVVISCIMCVAIMYIYGHRNYFQDIQMMLGFPPPLFFQICWRFVSPAIIFFILVFTVIQYPITAYNHYQYPGWAVAIGFLMALSSVLCIPLYAMFRLCRTDGADLLQRLKNATKPSRDWGPALLEHRTGRYAP

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	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.58 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	129157

fit	/app/data/saxs_computation/wf/8wfi/8wfi.fit
pddf	/app/data/pr_computation/wf/8wfi/8wfi.pr.out
profile	/app/data/saxs_computation/wf/8wfi/8wfi.dat

human glycine transporter 1 in complex with glycine in occluded conformation

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

Isoform GlyT-1B of Sodium- and chloride-dependent glycine transporter 1

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

冷冻电镜 EM 3D