SAXSdb — 3lcb

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

Isocitrate dehydrogenase kinase/phosphatase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Isocitrate dehydrogenase [NADP] × 1 （P08200） ADENOSINE MONOPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Isocitrate dehydrogenase [NADP] × 1 （P08200） ADENOSINE MONOPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Isocitrate dehydrogenase [NADP] × 6 （P08200） ADENOSINE MONOPHOSPHATE × 6 ADENOSINE-5'-TRIPHOSPHATE × 6 MAGNESIUM ION × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACEK_ECO5E
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–578； UniProt 1–578 Author chain B； PDBConstruct 1–578； UniProt 1–578

Isocitrate dehydrogenase [NADP]

Escherichia coli

UniProt P08200

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Isocitrate dehydrogenase kinase/phosphatase × 1 （B5Z0A8） ADENOSINE MONOPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Isocitrate dehydrogenase kinase/phosphatase × 1 （B5Z0A8） ADENOSINE MONOPHOSPHATE × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 12	Isocitrate dehydrogenase kinase/phosphatase × 6 （B5Z0A8） ADENOSINE MONOPHOSPHATE × 6 ADENOSINE-5'-TRIPHOSPHATE × 6 MAGNESIUM ION × 6 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	IDH_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–416； UniProt 1–416 Author chain D； PDBConstruct 1–416； UniProt 1–416

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	3lcb
Deposition date deposition_date	2010-01-10
Structure title title	The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.
Keywords keywords	KINASE PHOSPHATASE, GLYOXYLATE BYPASS, HYDROLASEPROTEIN PHOSPHATASE, TRICARBOXYLIC ACID CYCLE, Isocitrate, TRANSFERASE, HYDROLASE; TRANSFERASE, HYDROLASE
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.

3lcb__assembly_1__model_1

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

Download this curve (.dat)

3lcb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3lcb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	35.17 Å
Rg (electron density)	35.00 Å
Total Rg	35.37 Å
Atom count	7838
Residues	969
Excluded volume	139660 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3lcb__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3lcb__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3lcb__assembly_3__model_1`	dodecameric （12）	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	Isocitrate dehydrogenase kinase/phosphatase
Molecular weight formula_weight	67823.6 kDa
EC 编号 ec_number	2.7.11.5, 3.1.3.-
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	15771

MPRGLELLIAQTILQGFDAQYGRFLEVTSGAQQRFEQADWHAVQQAMKNRIHLYDHHVGLVVEQLRCITNGQSTDAEFLLRVKEHYTRLLPDYPRFEIAESFFNSVYCRLFDHRSLTPERLFIFSSQPERRFRTIPRPLAKDFHPDHGWESLLMRVISDLPLRLHWQNKSRDIHYIIRHLTETLGPENLSKSHLQVANELFYRNKAAWLVGKLITPSGTLPFLLPIHQTDDGELFIDTCLTTTAEASIVFGFARSYFMVYAPLPAALVEWLREILPGKTTAELYMAIGCQKHAKTESYREYLVYLQGCNEQFIEAPGIRGMVMLVFTLPGFDRVFKVIKDKFAPQKEMSAAHVRACYQLVKEHDRVGRMADTQEFENFVLEKRHISPALMELLLQEAAEKITDLGEQIVIRHLYIERRMVPLNIWLEQVEGQQLRDAIEEYGNAIRQLAAANIFPGDMLFKNFGVTRHGRVVFYDYDEICYMTEVNFRDIPPPRYPEDELASEPWYSVSPGDVFPEEFRHWLCADPRIGPLFEEMHADLFRADYWRALQNRIREGHVEDVYAYRRRQRFSVRYGEMLF

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83334
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Isocitrate dehydrogenase [NADP]
Molecular weight formula_weight	45809.6 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	C,D

MESKVVVPAQGKKITLQNGKLNVPENPIIPYIEGDGIGVDVTPAMLKVVDAAVEKAYKGERKISWMEIYTGEKSTQVYGQDVWLPAETLDLIREYRVAIKGPLTTPVGGGIRSLNVALRQELDLYICLRPVRYYQGTPSPVKHPELTDMVIFRENSEDIYAGIEWKADSADAEKVIKFLREEMGVKKIRFPEHCGIGIKPCSEEGTKRLVRAAIEYAIANDRDSVTLVHKGNIMKFTEGAFKDWGYQLAREEFGGELIDGGPWLKVKNPNTGKEIVIKDVIADAFLQQILLRPAEYDVIACMNLNGDYISDALAAQVGGIGIAPGANIGDECALFEATHGTAPKYAGQDKVNPGSIILSAEMMLRHMGWTEAADLIVKGMEGAINAKTVTYDFERLMDGAKLLKCSEFGDAIIENM

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE MONOPHOSPHATE
Molecular weight formula_weight	347.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	21

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3lcbc_
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.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

Domain ID domain_id	d3lcbd_
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.77.1.1 — Dimeric isocitrate & isopropylmalate dehydrogenases

CATH v4.4 (2 domains)

Domain ID domain_id	3lcbC00
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	3lcbD00
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	196.801 Å
Unit-cell length b length_b	196.801 Å
Unit-cell length c length_c	156.458 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1920
R_work r_work	0.1900
R_free r_free	0.2220

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

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

Isocitrate dehydrogenase kinase/phosphatase

State in the Current Structure

Other States of the Same Protein in the Database

Isocitrate dehydrogenase [NADP]

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

3lcb__assembly_1__model_1

3lcb__assembly_1__model_1 | I(q)

3lcb__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

The crystal structure of isocitrate dehydrogenase kinase/phosphatase in complex with its substrate, isocitrate dehydrogenase, from Escherichia coli.

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

Isocitrate dehydrogenase kinase/phosphatase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Isocitrate dehydrogenase [NADP]

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

3lcb__assembly_1__model_1

3lcb__assembly_1__model_1 | I(q)

3lcb__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 (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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)