SAXSdb — 4ld2

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

Cytidine and deoxycytidylate deaminase zinc-binding region

Nitrosomonas europaea

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 2 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE × 1 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q82Y41_NITEU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–195； UniProt 1–193 Author chain B； PDBConstruct 3–195； UniProt 1–193

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	4ld2
Deposition date deposition_date	2013-06-24
Structure title title	Crystal structure of NE0047 in complex with cytidine
Keywords keywords	CDA fold, deaminase, HYDROLASE; 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.

4ld2__assembly_1__model_1

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

Download this curve (.dat)

4ld2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4ld2__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.81 Å
Rg (electron density)	19.77 Å
Total Rg	20.59 Å
Atom count	2718
Residues	368
Excluded volume	48167 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4ld2__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 (5)

Entity 1 Entity 1 polymer

Description description	Cytidine and deoxycytidylate deaminase zinc-binding region
Molecular weight formula_weight	20586.5 kDa
EC 编号 ec_number	3.5.-.-
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	2945

GHMNDALHIGLPPFLVQANNEPRVLAAPEARMGYVLELVRANIAADGGPFAAAVFERDSGLLIAAGTNRVVPGRCSAAHAEILALSLAQAKLDTHDLSADGLPACELVTSAEPCVMCFGAVIWSGVRSLVCAARSDDVEAIGFDEGPRPENWMGGLEARGITVTTGLLRDAACALLREYNACNGVIYNARCGVHKGS

Source Source

Source organism organism	Nitrosomonas europaea
NCBI taxonomy ID ncbi_taxonomy_id	228410
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE
Molecular weight formula_weight	243.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	227

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4ld2a_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.2 — Deoxycytidylate deaminase-like

Domain ID domain_id	d4ld2b_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.97 — Cytidine deaminase-like
Superfamily Superfamily superfamily	c.97.1 — Cytidine deaminase-like
Family Family family	c.97.1.2 — Deoxycytidylate deaminase-like

CATH v4.4 (2 domains)

Domain ID domain_id	4ld2A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

Domain ID domain_id	4ld2B01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	140 — Cytidine Deaminase; domain 2
Homologous superfamily homologous superfamily	10 — Cytidine Deaminase, domain 2

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Unit-cell length a length_a	38.210 Å
Unit-cell length b length_b	74.550 Å
Unit-cell length c length_c	110.110 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	27.530 Å
R factor r_factor	—
R_work r_work	0.1986
R_free r_free	0.2181

Crystal structure of NE0047 in complex with cytidine

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

Cytidine and deoxycytidylate deaminase zinc-binding region

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

4ld2__assembly_1__model_1

4ld2__assembly_1__model_1 | I(q)

4ld2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal structure of NE0047 in complex with cytidine

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

Cytidine and deoxycytidylate deaminase zinc-binding region

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

4ld2__assembly_1__model_1

4ld2__assembly_1__model_1 | I(q)

4ld2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)