SAXSdb — 1itw

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

Isocitrate dehydrogenase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 ISOCITRIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 2 ISOCITRIC ACID × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 ISOCITRIC ACID × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	MANGANESE (II) ION × 1 ISOCITRIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IDH_AZOVI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–741； UniProt 1–741 Author chain B； PDBConstruct 1–741； UniProt 1–741 Author chain C； PDBConstruct 1–741； UniProt 1–741 Author chain D； PDBConstruct 1–741； UniProt 1–741

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	1itw
Deposition date deposition_date	2002-02-12
Structure title title	Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn
Keywords keywords	Greece key motif, 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.

1itw__assembly_2__model_1

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

Download this curve (.dat)

1itw__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1itw__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.47 Å
Rg (electron density)	26.44 Å
Total Rg	27.24 Å
Atom count	5663
Residues	740
Excluded volume	101130 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1itw__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1itw__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1itw__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1itw__assembly_4__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	Isocitrate dehydrogenase
Molecular weight formula_weight	80507.6 kDa
EC 编号 ec_number	1.1.1.42
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	24949

MSTPKIIYTLTDEAPALATYSLLPIIKAFTGSSGIAVETRDISLAGRLIATFPEYLTDTQKISDDLAELGKLATTPDANIIKLPNISASVPQLKAAIKELQQQGYKLPDYPEEPKTDTEKDVKARYDKIKGSAVNPVLREGNSDRRAPLSVKNYARKHPHKMGAWSADSKSHVAHMDNGDFYGSEKAALIGAPGSVKIELIAKDGSSTVLKAKTSVQAGEIIDSSVMSKNALRNFIAAEIEDAKKQGVLLSVHLKATMMKVSDPIMFGQIVSEFYKDALTKHAEVLKQIGFDVNNGIGDLYARIKTLPEAKQKEIEADIQAVYAQRPQLAMVNSDKGITNLHVPSDVIVDASMPAMIRDSGKMWGPDGKLHDTKAVIPDRCYAGVYQVVIEDCKQHGAFDPTTMGSVPNVGLMAQKAEEYGSHDKTFQIPADGVVRVTDESGKLLLEQSVEAGDIWRMCQAKDAPIQDWVKLAVNRARATNTPAVFWLDPARAHDAQVIAKVERYLKDYDTSGLDIRILSPVEATRFSLARIREGKDTISVTGNVLRDYLTDLFPIMELGTSAKMLSIVPLMSGGGLFETGAGGSAPKHVQQFLEEGYLRWDSLGEFLALAASLEHLGNAYKNPKALVLASTLDQATGKILDNNKSPARKVGEIDNRGSHFYLALYWAQALAAQTEDKELQAQFTGIAKALTDNETKIVGELAAAQGKPVDIAGYYHPNTDLTSKAMRPSATFNAALAPLA

Entity 2 Entity 2 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	ISOCITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2306

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1itwa_
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.77.1.2 — Monomeric isocitrate dehydrogenase

Domain ID domain_id	d1itwb_
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.77.1.2 — Monomeric isocitrate dehydrogenase

Domain ID domain_id	d1itwc_
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.77.1.2 — Monomeric isocitrate dehydrogenase

Domain ID domain_id	d1itwd_
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.77.1.2 — Monomeric isocitrate dehydrogenase

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Unit-cell length a length_a	110.405 Å
Unit-cell length b length_b	119.023 Å
Unit-cell length c length_c	128.217 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.01 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	—
R_work r_work	0.1930
R_free r_free	0.2280

Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn

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

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

1itw__assembly_2__model_1

1itw__assembly_2__model_1 | I(q)

1itw__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (2)

Crystal structure of the monomeric isocitrate dehydrogenase in complex with isocitrate and Mn

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

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

1itw__assembly_2__model_1

1itw__assembly_2__model_1 | I(q)

1itw__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

7. Citations (2)