2yfh

Structure of a Chimeric Glutamate Dehydrogenase

Method: X-RAY DIFFRACTION

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

GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE

CLOSTRIDIUM SYMBIOSUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	E7GGS1_CLOSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–200； UniProt 1–200 Author chain A； PDBConstruct 405–448； UniProt 407–450 Author chain B； PDBConstruct 1–200； UniProt 1–200 Author chain B； PDBConstruct 405–448； UniProt 407–450 Author chain C； PDBConstruct 1–200； UniProt 1–200 Author chain C； PDBConstruct 405–448； UniProt 407–450 Author chain D； PDBConstruct 1–200； UniProt 1–200 Author chain D； PDBConstruct 405–448； UniProt 407–450 Author chain E； PDBConstruct 1–200； UniProt 1–200 Author chain E； PDBConstruct 405–448； UniProt 407–450 Author chain F； PDBConstruct 1–200； UniProt 1–200 Author chain F； PDBConstruct 405–448； UniProt 407–450

GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE

CLOSTRIDIUM SYMBIOSUM

UniProt P00370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHE4_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 201–404； UniProt 202–405 Author chain B； PDBConstruct 201–404； UniProt 202–405 Author chain C； PDBConstruct 201–404； UniProt 202–405 Author chain D； PDBConstruct 201–404； UniProt 202–405 Author chain E； PDBConstruct 201–404； UniProt 202–405 Author chain F； PDBConstruct 201–404； UniProt 202–405

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	2yfh
Deposition date deposition_date	2011-04-05
Structure title title	Structure of a Chimeric Glutamate Dehydrogenase
Keywords keywords	OXIDOREDUCTASE, CHIMERA; OXIDOREDUCTASE
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.

2yfh__assembly_1__model_1

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

Download this curve (.dat)

2yfh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2yfh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.22 Å
Rg (electron density)	41.61 Å
Total Rg	42.01 Å
Atom count	20327
Residues	2677
Excluded volume	360700 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2yfh__assembly_1__model_1`	hexameric （6）	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 (2)

Entity 1 Entity 1 polymer

Description description	GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE
Molecular weight formula_weight	48429.8 kDa
EC 编号 ec_number	1.4.1.4, 1.4.1.3, 1.4.1.2
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	20640

MSKYVDRVIAEVEKKYADEPEFVQTVEEVLSSLGPVVDAHPEYEEVALLERMVIPERVIEFRVPWEDDNGKVHVNTGYRVQFNGAIGPYKGGLRFAPSVNLSIMKFLGFEQAFKDSLTTLPMGGAKGGSDFDPNGKSDREVMRFCQAFMTELYRHIGPDIDVPAGDLGVGAREIGYMYGQYRKIVGGFYNGVLTGKARSFGGSLIRPEATGYGLVYFTEAMLKRHGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVITASDSSGTVVDESGFTKEKLARLIEIKASRDGRVADYAKEFGLVYLEGQQPWSLPVDIALPCATQNELDVDAAHQLIANGVKAVAEGANMPTTIEATELFQQAGVLFAPGKAANAGGVATSGLEMAQNAARLGWKAEKVDARLHHIMTDIHDGSAAAAERYGLGYNLVAGANIVGFQKIADAMMAQGIAW

Source Source

Source organism organism	CLOSTRIDIUM SYMBIOSUM
NCBI taxonomy ID ncbi_taxonomy_id	1512
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	313

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6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2yfha1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d2yfha2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2yfhb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d2yfhb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2yfhc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d2yfhc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2yfhd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d2yfhd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2yfhe1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d2yfhe2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

Domain ID domain_id	d2yfhf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d2yfhf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.0 — automated matches

CATH v4.4 (18 domains)

Domain ID domain_id	2yfhA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	2yfhA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	2yfhA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2yfhB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	2yfhB02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	2yfhB03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2yfhC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	2yfhC02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	2yfhC03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2yfhD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	2yfhD02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	2yfhD03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2yfhE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	2yfhE02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	2yfhE03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

Domain ID domain_id	2yfhF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	2yfhF02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	2yfhF03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	100.102 Å
Unit-cell length b length_b	113.859 Å
Unit-cell length c length_c	109.581 Å
Unit-cell angle α angle_alpha	116.54 °
Unit-cell angle β angle_beta	101.54 °
Unit-cell angle γ angle_gamma	104.09 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.695 Å
Low-resolution limit resolution_low	36.524 Å
R factor r_factor	0.2184
R_work r_work	0.2150
R_free r_free	0.2823

Structure of a Chimeric Glutamate Dehydrogenase

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

GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE

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

2yfh__assembly_1__model_1

2yfh__assembly_1__model_1 | I(q)

2yfh__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Structure of a Chimeric Glutamate Dehydrogenase

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

GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

GLUTAMATE DEHYDROGENASE, NAD-SPECIFIC GLUTAMATE DEHYDROGENASE, GLUTAMATE DEHYDROGENASE

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

2yfh__assembly_1__model_1

2yfh__assembly_1__model_1 | I(q)

2yfh__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (1)