3s1c

Maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine

Method: X-RAY DIFFRACTION

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

Cytokinin dehydrogenase 1

Zea mays

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 FLAVIN-ADENINE DINUCLEOTIDE × 1 N-(3-methylbut-2-en-1-yl)adenosine × 1 GLYCEROL × 14 POLYETHYLENE GLYCOL (N=34) × 4 DI(HYDROXYETHYL)ETHER × 4 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CKX1_MAIZE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–516； UniProt 19–534

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	3s1c
Deposition date deposition_date	2011-05-15
Structure title title	Maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine
Keywords keywords	;OXIDOREDUCTASE, FAD BINDING PROTEIN, FLAVOPROTEIN, CYTOKININ OXIDASE/DEHYDROGENASE, CYTOKININ BINDING, GLYCOSYLATION, COVALENT FLAVINATION ;; 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.

3s1c__assembly_1__model_1

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

Download this curve (.dat)

3s1c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3s1c__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.84 Å
Rg (electron density)	22.89 Å
Total Rg	23.88 Å
Atom count	4085
Residues	498
Excluded volume	72512 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3s1c__assembly_1__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 (9)

Entity 1 Entity 1 polymer

Description description	Cytokinin dehydrogenase 1
Molecular weight formula_weight	55357.2 kDa
EC 编号 ec_number	1.5.99.12
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4414

LAAGTPALGDDRGRPWPASLAALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTADLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWTDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRLVYTDFAAFSADQERLTAPRPGGGGASFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNYDNATAAAAAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGPLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSSVAPNDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN

Source Source

Source organism organism	Zea mays
Common name common_name	maize
NCBI taxonomy ID ncbi_taxonomy_id	4577
Host organism host_organism	Yarrowia lipolytica

Entity 2 Entity 2 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	FLAVIN-ADENINE DINUCLEOTIDE
Molecular weight formula_weight	785.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	N-(3-methylbut-2-en-1-yl)adenosine
Molecular weight formula_weight	335.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 6 Entity 6 non-polymer

Description description	POLYETHYLENE GLYCOL (N=34)
Molecular weight formula_weight	1529.8 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	324

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3s1ca1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamily	d.145.1 — FAD-binding/transporter-associated domain-like
Family Family family	d.145.1.0 — automated matches

Domain ID domain_id	d3s1ca2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.58 — Ferredoxin-like
Superfamily Superfamily superfamily	d.58.32 — FAD-linked oxidases, C-terminal domain
Family Family family	d.58.32.4 — Cytokinin dehydrogenase 1

CATH v4.4 (3 domains)

Domain ID domain_id	3s1cA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily	10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2

Domain ID domain_id	3s1cA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3s1cA03
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — FAD-linked oxidases, C-terminal domain

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Unit-cell length a length_a	250.950 Å
Unit-cell length b length_b	50.620 Å
Unit-cell length c length_c	51.400 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.97 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.090 Å
Low-resolution limit resolution_low	32.500 Å
R factor r_factor	0.2148
R_work r_work	0.2128
R_free r_free	0.2524

Maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine

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

Cytokinin dehydrogenase 1

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

3s1c__assembly_1__model_1

3s1c__assembly_1__model_1 | I(q)

3s1c__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Maize cytokinin oxidase/dehydrogenase complexed with N6-isopentenyladenosine

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

Cytokinin dehydrogenase 1

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

3s1c__assembly_1__model_1

3s1c__assembly_1__model_1 | I(q)

3s1c__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 (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

7. Citations (1)