SAXSdb — 4iem

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

DNA-(apurinic or apyrimidinic site) lyase

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(GPCPTPAPC)-3') ; × 1 ;DNA (5'-D(P(3DR)PGPAPTPCPG)-3') ; × 1 ;DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3') ; × 1 MAGNESIUM ION × 3 SODIUM ION × 4 water × 4	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(GPCPTPAPC)-3') ; × 1 ;DNA (5'-D(P(3DR)PGPAPTPCPG)-3') ; × 1 ;DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3') ; × 1 MAGNESIUM ION × 1 SODIUM ION × 3 water × 4	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(GPCPTPAPC)-3') ; × 1 ;DNA (5'-D(P(3DR)PGPAPTPCPG)-3') ; × 1 ;DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3') ; × 1 MAGNESIUM ION × 2 water × 4	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 3	;DNA (5'-D(GPCPTPAPC)-3') ; × 1 ;DNA (5'-D(P(3DR)PGPAPTPCPG)-3') ; × 1 ;DNA (5'-D(CPGPAPTPCPGPGPTPAPGPC)-3') ; × 1 MAGNESIUM ION × 1 SODIUM ION × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	APEX1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–317； UniProt 2–318 Author chain B； PDBConstruct 1–317； UniProt 2–318 Author chain C； PDBConstruct 1–317； UniProt 2–318 Author chain D； PDBConstruct 1–317； UniProt 2–318

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	4iem
Deposition date deposition_date	2012-12-13
Structure title title	Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+
Keywords keywords	metalloprotein, DNA damage, DNA repair, base excision repair, protein-DNA, REF1, nuclease, HYDROLASE, LYASE-DNA complex; HYDROLASE, LYASE/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.

4iem__assembly_1__model_1

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

Download this curve (.dat)

4iem__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4iem__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.22 Å
Rg (electron density)	19.00 Å
Total Rg	20.04 Å
Atom count	5091
Residues	299
Excluded volume	45984 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4iem__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4iem__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4iem__assembly_3__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4iem__assembly_4__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	DNA-(apurinic or apyrimidinic site) lyase
Molecular weight formula_weight	35475.3 kDa
EC 编号 ec_number	3.1.-.-, 4.2.99.18
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	20539

PKRGKKGAVAEDGDELRTEPEAKKSKTAAKKNDKEAAGEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLLPALCDSKIRSKALGSDHCPITLYLAL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(GPCPTPAP*C)-3') ;
Molecular weight formula_weight	1480.0 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,H,K,N

GCTAC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(P(3DR)PGPAPTPCPG)-3') ;
Molecular weight formula_weight	1700.1 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,I,L,O

NGATCG

Entity 4 Entity 4 polymer

Description description	;DNA (5'-D(CPGPAPTPCPGPGPTPAPGP*C)-3') ;
Molecular weight formula_weight	3374.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	G,J,M,P

CGATCGGTAGC

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	7

Entity 6 Entity 6 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	272

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4iemA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

Domain ID domain_id	4iemB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

Domain ID domain_id	4iemC00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

Domain ID domain_id	4iemD00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	10 — Deoxyribonuclease I; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease/exonuclease/phosphatase

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Unit-cell length a length_a	104.639 Å
Unit-cell length b length_b	74.090 Å
Unit-cell length c length_c	112.138 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.394 Å
Low-resolution limit resolution_low	29.643 Å
R factor r_factor	0.2099
R_work r_work	0.2079
R_free r_free	0.2462

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

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

DNA-(apurinic or apyrimidinic site) lyase

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

4iem__assembly_1__model_1

4iem__assembly_1__model_1 | I(q)

4iem__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Human apurinic/apyrimidinic endonuclease (APE1) with product DNA and Mg2+

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

DNA-(apurinic or apyrimidinic site) lyase

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

4iem__assembly_1__model_1

4iem__assembly_1__model_1 | I(q)

4iem__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 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)