5w0u

Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP

Method: X-RAY DIFFRACTION

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

Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPTPTPCPAPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPTPGPAPAPC)-3') ; × 1 ZINC ION × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 CALCIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with all polymers
2	Insufficient information	Monomer	Protein 1	ZINC ION × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MALE_ECO57
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–367； UniProt 27–392 Author chain B； PDBConstruct 2–367； UniProt 27–392

Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase

Homo sapiens

UniProt Q9GZX7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1 DNA 2	;DNA (5'-D(GPTPTPCPAPAPGPGPCPCPAPG)-3') ; × 1 ;DNA (5'-D(CPTPGPGPCPCPTPTPGPAPAPC)-3') ; × 1 ZINC ION × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 CALCIUM ION × 1 GLYCEROL × 1 water × 1	Consistent with all polymers
2	Insufficient information	Monomer	Protein 1	ZINC ION × 1 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AICDA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 381–549； UniProt 13–181 Author chain B； PDBConstruct 381–549； UniProt 13–181

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	5w0u
Deposition date deposition_date	2017-05-31
Structure title title	Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP
Keywords keywords	Class switch recombination, Cytidine deaminase, HYDROLASE-DNA complex; HYDROLASE/DNA
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.

5w0u__assembly_1__model_1

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

Download this curve (.dat)

5w0u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5w0u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.95 Å
Rg (electron density)	30.34 Å
Total Rg	31.16 Å
Atom count	4809
Residues	566
Excluded volume	84075 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5w0u__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5w0u__assembly_2__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 (8)

Entity 1 Entity 1 polymer

Description description	Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase
Molecular weight formula_weight	61659.9 kDa
EC 编号 ec_number	3.5.4.38
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,A
Atom count atom_count	9130

MKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPAAAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLLPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKYAAGKYDIKDVGVDNAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDTSAVNYGVTVLPTFKGQPSKPFVGVLSAGINAASPNKELAKEFLENYLLTDEGLEAVNKDKPLGAVALKSYEEELAKDPRIAATMENAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALAAAQTNAAAEFMDPATFTYQFKNVRWAKGRRETYLCYVVKRRDSATSESLDFGYLRNKNGCHVALLFLRYISDWDLDPGRCYRVTWFTSWSPCYDCARHVADFLRGNPNLSLRIFTARLYFCEDRKAEPEGLRRLAEAGVQIAIMTYKDYEYCWNTFVENHERTFKAWEGLHENSVRLSRQLRRILQ

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPTPTPCPAPAPGPGPCPCPAPG)-3') ;
Molecular weight formula_weight	3687.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GTTCAAGGCCAG

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(CPTPGPGPCPCPTPTPGPAPAPC)-3') ;
Molecular weight formula_weight	3638.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G

CTGGCCTTGAAC

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	307.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	2

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5w0uA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	5w0uA02
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	5w0uB01
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	125.005 Å
Unit-cell length b length_b	39.777 Å
Unit-cell length c length_c	153.935 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.14 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	153.935 Å
R factor r_factor	0.2521
R_work r_work	0.2509
R_free r_free	0.2814

Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP

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

Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase

State in the Current Structure

Other States of the Same Protein in the Database

Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase

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

5w0u__assembly_1__model_1

5w0u__assembly_1__model_1 | I(q)

5w0u__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP

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

Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Maltose-binding periplasmic protein,Single-stranded DNA cytosine deaminase

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

5w0u__assembly_1__model_1

5w0u__assembly_1__model_1 | I(q)

5w0u__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer 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 water

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)