1z56

Co-Crystal Structure of Lif1p-Lig4p

Method: X-RAY DIFFRACTION

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

Ligase interacting factor 1

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	DNA ligase IV × 1 （Q08387） Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 2 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LIF1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–246； UniProt 1–246 Author chain B； PDBConstruct 1–246； UniProt 1–246

DNA ligase IV

Saccharomyces cerevisiae

UniProt Q08387

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 11	Ligase interacting factor 1 × 2 （P53150） Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 2 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1 Ligase interacting factor 1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DNL4_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–263； UniProt 681–944

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	1z56
Deposition date deposition_date	2005-03-17
Structure title title	Co-Crystal Structure of Lif1p-Lig4p
Keywords keywords	DNA Repair, BRCT, NHEJ, Xrcc4, DNA Ligase, Coiled-coil, LIGASE; LIGASE
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.

1z56__assembly_1__model_1

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

Download this curve (.dat)

1z56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1z56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.27 Å
Rg (electron density)	44.00 Å
Total Rg	43.80 Å
Atom count	4164
Residues	557
Excluded volume	75201 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1z56__assembly_1__model_1`	undecameric （11）	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	Ligase interacting factor 1
Molecular weight formula_weight	28674.8 kDa
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	4164

MSQLTEFISCIPVVNEEQNEEDERGLCKIQIEDGAMLETLDENSLSGLRIEKMLVSEGTGIFSKSSFGINDLRIFTGENIDEESKKYVWYELLKMLTGHKVYIASLDEKVVFTKWTCRMQDDEVWKVVMELESSAIIRKIAELTLHPVKKGEIDLFEMADKLYKDICCVNDSYRNIKESDSSNRNRVEQLARERELLDKLLETRDERTRAMMVTLLNEKKKKIRELHEILRQNNIKLSDDDVLDSA

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21

Entity 2 Entity 2 polymer

Description description	DNA ligase IV
Molecular weight formula_weight	30366.1 kDa
EC 编号 ec_number	6.5.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

PISNIFAGLLFYVLSDYVTEDTGIRITRAELEKTIVEHGGKLIYNVILKRHSIGDVRLISCKTTTECKALIDRGYDILHPNWVLDCIAYKRLILIEPNYCFNVSQKMRAVAEKRVDCLGDSFENDISETKLSSLYKSQLSLPPMGELEIDSEVRRFPLFLFSNRIAYVPRRKISTEDDIIEMKIKLFGGKITDQQSLCNLIIIPYTDPILRKDCMNEVHEKIKEQIKASDTIPKIARVVAPEWVDHSINENCQVPEEDFPVVNY

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	698.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

XXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	613.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,H

XXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	3847.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 6 Entity 6 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	3166.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 7 Entity 7 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	2571.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 8 Entity 8 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	1720.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

XXXXXXXXXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 9 Entity 9 polymer

Description description	Ligase interacting factor 1
Molecular weight formula_weight	1124.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

XXXXXXXXXXXXX

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	1z56A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	1z56B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	370 —

Domain ID domain_id	1z56C01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10190 — BRCT domain

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Unit-cell length a length_a	247.617 Å
Unit-cell length b length_b	247.617 Å
Unit-cell length c length_c	98.416 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	24

Space group space_group	P 64 2 2
Space-group number int_tables_number	181
Crystal system crystal_system	—

Resolution resolution	3.920 Å
Low-resolution limit resolution_low	49.200 Å
R factor r_factor	0.4030
R_work r_work	0.4000
R_free r_free	0.4670

Co-Crystal Structure of Lif1p-Lig4p

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

Ligase interacting factor 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

DNA ligase IV

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

1z56__assembly_1__model_1

1z56__assembly_1__model_1 | I(q)

1z56__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source

Entity 6 Entity 6 polymer

Polymer Polymer

Source Source

Entity 7 Entity 7 polymer

Polymer Polymer

Source Source

Entity 8 Entity 8 polymer

Polymer Polymer

Source Source

Entity 9 Entity 9 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

7. Citations (1)