SAXSdb — 2dbx

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

Gamma-glutamyltranspeptidase

Escherichia coli K12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 1 CALCIUM ION × 1 GLUTAMIC ACID × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	CALCIUM ION × 1 GLUTAMIC ACID × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GGT_ECOLI
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–366； UniProt 25–390 Author chain C； PDBConstruct 1–366； UniProt 25–390 Author chain B； PDBConstruct 1–190； UniProt 391–580 Author chain D； PDBConstruct 1–190； UniProt 391–580

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	2dbx
Deposition date deposition_date	2005-12-16
Structure title title	Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Complexed with L-Glutamate
Keywords keywords	gamma-glutamyltransferase, ggt, gamma-gtp, glutathione, Transferase; TRANSFERASE
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.

2dbx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2dbx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2dbx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.08 Å
Rg (electron density)	22.16 Å
Total Rg	22.97 Å
Atom count	4079
Residues	525
Excluded volume	72695 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2dbx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2dbx__assembly_2__model_1`	dimeric （2）	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	Gamma-glutamyltranspeptidase
Molecular weight formula_weight	39827.1 kDa
EC 编号 ec_number	2.3.2.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8959

AAPPAPPVSYGVEEDVFHPVRAKQGMVASVDATATQVGVDILKEGGNAVDAAVAVGYALAVTHPQAGNLGGGGFMLIRSKNGNTTAIDFREMAPAKATRDMFLDDQGNPDSKKSLTSHLASGTPGTVAGFSLALDKYGTMPLNKVVQPAFKLARDGFIVNDALADDLKTYGSEVLPNHENSKAIFWKEGEPLKKGDTLVQANLAKSLEMIAENGPDEFYKGTIAEQIAQEMQKNGGLITKEDLAAYKAVERTPISGDYRGYQVYSMPPPSSGGIHIVQILNILENFDMKKYGFGSADAMQIMAEAEKYAYADRSEYLGDPDFVKVPWQALTNKAYAKSIADQIDINKAKPSSEIRPGKLAPYESNQ

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Gamma-glutamyltranspeptidase
Molecular weight formula_weight	20263.0 kDa
EC 编号 ec_number	2.3.2.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

TTHYSVVDKDGNAVAVTYTLNTTFGTGIVAGESGILLNNQMDDFSAKPGVPNVYGLVGGDANAVGPNKRPLSSMSPTIVVKDGKTWLVTGSPGGSRIITTVLQMVVNSIDYGLNVAEATNAPRFHHQWLPDELRVEKGFSPDTLKLLEAKGQKVALKEAMGSTQSIMVGPDGELYGASDPRSVDDLTAGY

Source Source

Source organism organism	Escherichia coli K12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	795

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2dbx.1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.6 — Gamma-glutamyltranspeptidase-like

Domain ID domain_id	d2dbx.2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.153 — Ntn hydrolase-like
Superfamily Superfamily superfamily	d.153.1 — N-terminal nucleophile aminohydrolases (Ntn hydrolases)
Family Family family	d.153.1.6 — Gamma-glutamyltranspeptidase-like

CATH v4.4 (4 domains)

Domain ID domain_id	2dbxA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	130 — Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain

Domain ID domain_id	2dbxB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	40 — Gamma-glutamyltranspeptidase, small (S) subunit

Domain ID domain_id	2dbxC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	246 — Serum Albumin; Chain A, Domain 1
Homologous superfamily homologous superfamily	130 — Gamma-glutamyltranspeptidase, large (L) subunit, C-terminal domain

Domain ID domain_id	2dbxD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	20 — Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1
Homologous superfamily homologous superfamily	40 — Gamma-glutamyltranspeptidase, small (S) subunit

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Unit-cell length a length_a	77.700 Å
Unit-cell length b length_b	126.500 Å
Unit-cell length c length_c	129.200 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	46.240 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2120

Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Complexed with L-Glutamate

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

Gamma-glutamyltranspeptidase

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

2dbx__assembly_2__model_1

2dbx__assembly_2__model_1 | I(q)

2dbx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Gamma-glutamyltranspeptidase from Escherichia coli Complexed with L-Glutamate

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

Gamma-glutamyltranspeptidase

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

2dbx__assembly_2__model_1

2dbx__assembly_2__model_1 | I(q)

2dbx__assembly_2__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

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 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (1)