SAXSdb — 2e5m

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

409aa long hypothetical NADP-dependent isocitrate dehydrogenase

Sulfolobus tokodaii str. 7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96YK6_SULTO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–409； UniProt 1–409 Author chain B； PDBConstruct 1–409； UniProt 1–409

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	2e5m
Deposition date deposition_date	2006-12-22
Structure title title	Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7
Keywords keywords	NADP-dependent isocitrate dehydrogenase, OXIDOREDUCTASE; 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.

2e5m__assembly_1__model_1

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

Download this curve (.dat)

2e5m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2e5m__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.66 Å
Rg (electron density)	29.00 Å
Total Rg	29.77 Å
Atom count	6542
Residues	806
Excluded volume	117510 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2e5m__assembly_1__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 (3)

Entity 1 Entity 1 polymer

Description description	409aa long hypothetical NADP-dependent isocitrate dehydrogenase
Molecular weight formula_weight	46558.9 kDa
EC 编号 ec_number	1.1.1.42
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6947

MLYKEPEDGEKIKFDKGKWIVPNKPVILYIEGDGIGPEITNAAIKVINKAVERAYGSSREIKWLEVYAGEKAEKLVNDRFPKETQEMLLKYRVVLKGPLETPIGKGWKSVNVAIRLMLDLYANIRPVKYIEGLESPLKHPEKVDMIIFRENTDDLYRGIEYPFNSEEAKKIRDFLRKELKVEIEDDTGIGIKVMSKYKTQRITRLAIQYAIEHKRKKVTIMHKGNVMKYTEGAFREWAYEVALKEYRDFIVTEEEINQGKPDQGKIILNDRIADNMFQQIIIRPEEYDIILAPNVNGDYISDAAGALIGNIGMLGGANIGDEGGMFEAIHGTAPKYAGKNVANPTGIIKAGELMLRWMGWNEAADLIEKAINMAIRDKKVTQDIARFMGVKALGTKEYADELIKIMDTI

Source Source

Source organism organism	Sulfolobus tokodaii str. 7
NCBI taxonomy ID ncbi_taxonomy_id	273063
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	743.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	405

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2e5ma_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.0 — automated matches

Domain ID domain_id	d2e5mb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.77 — Isocitrate/Isopropylmalate dehydrogenase-like
Superfamily Superfamily superfamily	c.77.1 — Isocitrate/Isopropylmalate dehydrogenase-like
Family Family family	c.77.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2e5mA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

Domain ID domain_id	2e5mB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	718 — Isopropylmalate Dehydrogenase
Homologous superfamily homologous superfamily	10 — Isopropylmalate Dehydrogenase

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Unit-cell length a length_a	74.780 Å
Unit-cell length b length_b	88.110 Å
Unit-cell length c length_c	75.670 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.36 °
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	2.400 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2790

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7

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

409aa long hypothetical NADP-dependent isocitrate 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

2e5m__assembly_1__model_1

2e5m__assembly_1__model_1 | I(q)

2e5m__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7

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

409aa long hypothetical NADP-dependent isocitrate 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

2e5m__assembly_1__model_1

2e5m__assembly_1__model_1 | I(q)

2e5m__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)