SAXSdb — 4nan

▼

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

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

Arabidopsis thaliana

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	2-bromo-6-(3,4,5-tribromo-1H-pyrrol-2-yl)phenol × 2 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 CADMIUM ION × 8 POTASSIUM ION × 12 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISPD_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–228； UniProt 76–302

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4nan
Deposition date deposition_date	2013-10-22
Structure title title	Arabidopsis thaliana IspD in complex with tetrabromo-pseudilin
Keywords keywords	;herbicide, anti-infectives, pseudilin, natural product, drug discovery, allosteric inhibition, Rossmann Fold, Transferase, TRANSFERASE-TRANSFERASE INHIBITOR complex ;; TRANSFERASE/TRANSFERASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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.

4nan__assembly_1__model_1

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

Download this curve (.dat)

4nan__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4nan__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.29 Å
Rg (electron density)	25.37 Å
Total Rg	26.21 Å
Atom count	3324
Residues	416
Excluded volume	61258 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4nan__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
Molecular weight formula_weight	25430.2 kDa
EC 编号 ec_number	2.7.7.60
Mutation mutation	R149S
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	1762

MEKSVSVILLAGGQGKRMKMSMPKQYIPLLGQPIALYSFFTFSRMPEVKEIVVVCDPFFRDIFEEYEESIDVDLSFAIPGKERQDSVYSGLQEIDVNSELVCIHDSARPLVNTEDVEKVLKDGSAVGAAVLGVPAKATIKEVNSDSLVVKTLDRKTLWEMQTPQVIKPELLKKGFELVKSEGLEVTDDVSIVEYLKHPVYVSQGSYTNIKVTTPDDLLLAERILSEDS

Source Source

Source organism organism	Arabidopsis thaliana
Common name common_name	mouse-ear cress, thale-cress
NCBI taxonomy ID ncbi_taxonomy_id	3702
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	2-bromo-6-(3,4,5-tribromo-1H-pyrrol-2-yl)phenol
Molecular weight formula_weight	474.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CADMIUM ION
Molecular weight formula_weight	112.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

▼

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4nana_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.68 — Nucleotide-diphospho-sugar transferases
Superfamily Superfamily superfamily	c.68.1 — Nucleotide-diphospho-sugar transferases
Family Family family	c.68.1.13 — Cytidylytransferase

CATH v4.4 (1 domains)

Domain ID domain_id	4nanA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	550 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A
Homologous superfamily homologous superfamily	10 — Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A

▶

Unit-cell length a length_a	75.120 Å
Unit-cell length b length_b	75.120 Å
Unit-cell length c length_c	224.130 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	18

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2088
R_work r_work	0.2067
R_free r_free	0.2472

Arabidopsis thaliana IspD in complex with tetrabromo-pseudilin

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

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

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

4nan__assembly_1__model_1

4nan__assembly_1__model_1 | I(q)

4nan__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Arabidopsis thaliana IspD in complex with tetrabromo-pseudilin

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

2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic

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

4nan__assembly_1__model_1

4nan__assembly_1__model_1 | I(q)

4nan__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (1)