SAXSdb — 6zpl

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

Sodium- and chloride-dependent glycine transporter 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Endoglucanase H × 1 （P16218） Sybody Sb_GlyT1#7 × 2 [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 SODIUM ION × 2 CHLORIDE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SC6A9_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–576； UniProt 92–684 Author chain B； PDBConstruct 1–576； UniProt 92–684

Endoglucanase H

Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)

UniProt P16218

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Sodium- and chloride-dependent glycine transporter 1 × 2 （P48067） Sybody Sb_GlyT1#7 × 2 [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 SODIUM ION × 2 CHLORIDE ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GUNH_HUNT2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–273； UniProt 31–303

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	6zpl
Deposition date deposition_date	2020-07-08
Structure title title	Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.
Keywords keywords	;secondary active transport, neurotransmitter-sodium symport, amino acid transport, SLC6A9, inward open state, inhibitor bound complex, MEMBRANE PROTEIN ;; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6zpl__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6zpl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zpl__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	43.29 Å
Rg (electron density)	42.20 Å
Total Rg	42.53 Å
Atom count	24610
Residues	1561
Excluded volume	225050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zpl__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Sodium- and chloride-dependent glycine transporter 1
Molecular weight formula_weight	64730.4 kDa
Mutation 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. ;
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	24610

TKRDQNLKRGNWGNQIEFVLTSVGYAVGLGNVWRFPYLCYRNGGGAFMFPYFIMLIFCGIPAFFMELSFGQFASQGCLGVWRISPMFKGVGYGMMVVSTYIGIYYNVVICIAFYYFFSSMTHVLPWAYCNNPWNTHDCAGVLDASNLTHSLQRTSPSEEYWRLYVLKLSDDIGNFGEVRLPLLGCLGVAWLVVFLCLIRGVKSSGKVVYFTATFPYVVLTILFVRGVTLEGAFDGIMYYLTPQWDKILEAKVWGDAASQAFYSLGCAWGGLITMASYNKFHNNCYRDSVIISITNCATSVYAGFVIFSILGFMANHLGVDVSRVADHGPGLAFVAYPEALTLLPISPLWSLLFFFMLILLGLGTQFCLLETLVTAIVDEVGNEWILQKKTYVTLGVAVAGFLLGIPLTSQAGIYWLLLMDNYAASFSLVVISCIMCVAIMYIYGHRNYFQDIQMMLGFPPPLFFQICWRFVSPAIIFFILVFTVIQYQPITYNHYQYPGWAVAIGFLMALSSVLCIPLYAMFRLARTDGDTLLQRLKNATKPSRDWGPALLEHRTGRYAPTIAPSPEDGFEVQPLH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Endoglucanase H
Molecular weight formula_weight	31163.5 kDa
EC 编号 ec_number	3.2.1.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

LKIGAWVGTQPSESAIKSFQELQGRKLDIVHQFINWSTDFSWVRPYADAVYNNGSILMITWEPWEYNTVDIKNGKADAYITRMAQDMKAYGKEIWLRPLHAANGDWYPWAIGYSSRVNTNETYIAAFRHIVDIFRANGATNVKWVFNVNCDNVGNGTSYLGHYPGDNYVDYTSIDGYNWGTTQSWGSQWQSFDQVFSRAYQALASINKPIIIAEFASAEIGGNKARWITEAYNSIRTSYNKVIAAVWFHENKETDWRINSSPEALAAYREAIG

Source Source

Source organism organism	Hungateiclostridium thermocellum (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)
NCBI taxonomy ID ncbi_taxonomy_id	203119
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Sybody Sb_GlyT1#7
Molecular weight formula_weight	13303.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F

QVQLVESGGGLVQAGGSLRLSCAASGFPVYAYEMYWYRQAPGKEREWVAAISSSGTWAGYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCNVKDWGASWAYYDYWGQGTQVTVS

Source Source

Source organism organism	unidentified
NCBI taxonomy ID ncbi_taxonomy_id	32644
Host organism host_organism	Escherichia coli MC1061

Entity 4 Entity 4 non-polymer

Description description	[5-fluoranyl-6-(oxan-4-yloxy)-1,3-dihydroisoindol-2-yl]-[5-methylsulfonyl-2-[2,2,3,3,3-pentakis(fluoranyl)propoxy]phenyl]methanone
Molecular weight formula_weight	567.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6zplE01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6zplF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	116.410 Å
Unit-cell length b length_b	69.710 Å
Unit-cell length c length_c	149.430 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.86 °
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	3.945 Å
Low-resolution limit resolution_low	29.070 Å
R factor r_factor	0.2774
R_work r_work	0.2766
R_free r_free	0.2914

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.

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

Sodium- and chloride-dependent glycine transporter 1

State in the Current Structure

Other States of the Same Protein in the Database

Endoglucanase H

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6zpl__assembly_1__model_1

6zpl__assembly_1__model_1 | I(q)

6zpl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Inward-open structure of human glycine transporter 1 in complex with a benzoylisoindoline inhibitor, sybody Sb_GlyT1#7 and bound Na and Cl ions.

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

Sodium- and chloride-dependent glycine transporter 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Endoglucanase H

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6zpl__assembly_1__model_1

6zpl__assembly_1__model_1 | I(q)

6zpl__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)