6mxx

Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991

Method: X-RAY DIFFRACTION

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

TP53-binding protein 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 3 N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 FORMIC ACID × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 6 N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 FORMIC ACID × 3 water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 N-[3-(tert-butylamino)propyl]-3-iodobenzamide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TP53B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–123； UniProt 1484–1603 Author chain B； PDBConstruct 4–123； UniProt 1484–1603 Author chain C； PDBConstruct 4–123； UniProt 1484–1603 Author chain D； PDBConstruct 4–123； UniProt 1484–1603 Author chain E； PDBConstruct 4–123； UniProt 1484–1603 Author chain F； PDBConstruct 4–123； UniProt 1484–1603 Author chain G； PDBConstruct 4–123； UniProt 1484–1603 Author chain H； PDBConstruct 4–123； UniProt 1484–1603 Author chain I； PDBConstruct 4–123； UniProt 1484–1603 Author chain J； PDBConstruct 4–123； UniProt 1484–1603

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	6mxx
Deposition date deposition_date	2018-10-31
Structure title title	Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991
Keywords keywords	53BP1, Tandem Tudor domains, Small molecule inhibitor, DNA damage response, Class switch recombination, Protein Binding; PROTEIN BINDING
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.

6mxx__assembly_1__model_1

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

Download this curve (.dat)

6mxx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6mxx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.86 Å
Rg (electron density)	17.80 Å
Total Rg	18.73 Å
Atom count	3816
Residues	239
Excluded volume	34385 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6mxx__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6mxx__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6mxx__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6mxx__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`6mxx__assembly_5__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	TP53-binding protein 1
Molecular weight formula_weight	13944.8 kDa
Source method src_method	man
Copy count entity_count	10

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	20865

GHMNSFVGLRVVAKWSSNGYFYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSEDEYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQYGLG

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 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	21

Entity 3 Entity 3 non-polymer

Description description	N-[3-(tert-butylamino)propyl]-3-iodobenzamide
Molecular weight formula_weight	360.2 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	411

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6. Fold Classification (SCOP + CATH) 42 domains

SCOP 2.08 (22 domains)

Domain ID domain_id	d6mxxa1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxa2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxb1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxb2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxc1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxc2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxc3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6mxxd1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxd2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxe1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxe2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxf1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxf2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxg1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxg2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxh1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxh2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxi1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxi2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxj1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxj2
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.9 — Tudor/PWWP/MBT
Family Family family	b.34.9.1 — Tudor domain

Domain ID domain_id	d6mxxj3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (20 domains)

Domain ID domain_id	6mxxA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxB02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxC01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxC02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxD01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxD02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxE01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxE02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxF01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxF02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxG01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxG02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxH01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxH02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxI01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxI02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

Domain ID domain_id	6mxxJ01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	6mxxJ02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	30 —

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Unit-cell length a length_a	68.940 Å
Unit-cell length b length_b	159.430 Å
Unit-cell length c length_c	181.190 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	40

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

Resolution resolution	2.298 Å
Low-resolution limit resolution_low	48.140 Å
R factor r_factor	0.2069
R_work r_work	0.2063
R_free r_free	0.2315

Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991

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

TP53-binding protein 1

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

6mxx__assembly_1__model_1

6mxx__assembly_1__model_1 | I(q)

6mxx__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 (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) 42 domains

SCOP 2.08 (22 domains)

CATH v4.4 (20 domains)

7. Citations (1)

Structure of 53BP1 tandem Tudor domains in complex with small molecule UNC2991

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

TP53-binding protein 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6mxx__assembly_1__model_1

6mxx__assembly_1__model_1 | I(q)

6mxx__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 (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) 42 domains

SCOP 2.08 (22 domains)

CATH v4.4 (20 domains)

7. Citations (1)