SAXSdb — 5hda

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

Zinc finger MYND domain-containing protein 11

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Epstein-Barr nuclear antigen 2 × 2 （P12978） ZINC ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ZMY11_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–124； UniProt 480–602 Author chain C； PDBConstruct 2–124； UniProt 480–602

Epstein-Barr nuclear antigen 2

OrganismNot specified

UniProt P12978

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Zinc finger MYND domain-containing protein 11 × 2 （Q15326） ZINC ION × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EBNA2_EBVB9
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–9； UniProt 381–389 Author chain D； PDBConstruct 1–9； UniProt 381–389

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	5hda
Deposition date deposition_date	2016-01-05
Structure title title	Crystal Structure of the BS69 coiled coil-MYND domains bound to an EBNA2 PXLXP motif
Keywords keywords	BS69, EBNA2, MYND, zMYND11, coiled-coil, IMMUNE SYSTEM; IMMUNE SYSTEM
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.

5hda__assembly_1__model_1

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

Download this curve (.dat)

5hda__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5hda__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.70 Å
Rg (electron density)	41.99 Å
Total Rg	41.28 Å
Atom count	2079
Residues	255
Excluded volume	36569 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5hda__assembly_1__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 (4)

Entity 1 Entity 1 polymer

Description description	Zinc finger MYND domain-containing protein 11
Molecular weight formula_weight	15187.5 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	2186

SDRMKSDHKRETERVVREALEKLRSEMEEEKRQAVNKAVANMQGEMDRKCKQVKEKCKEEFVEEIKKLATQHKQLISQTKKKQWCYNCEEEAMYHCCWNTSYCSIKCQQEHWHAEHKRTCRRKR

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	Epstein-Barr nuclear antigen 2
Molecular weight formula_weight	972.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SMPELSPVL

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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Unit-cell length a length_a	58.456 Å
Unit-cell length b length_b	38.190 Å
Unit-cell length c length_c	82.690 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	44.600 Å
R factor r_factor	0.2241
R_work r_work	0.2221
R_free r_free	0.2616

Crystal Structure of the BS69 coiled coil-MYND domains bound to an EBNA2 PXLXP motif

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

Zinc finger MYND domain-containing protein 11

State in the Current Structure

Other States of the Same Protein in the Database

Epstein-Barr nuclear antigen 2

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

5hda__assembly_1__model_1

5hda__assembly_1__model_1 | I(q)

5hda__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal Structure of the BS69 coiled coil-MYND domains bound to an EBNA2 PXLXP motif

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

Zinc finger MYND domain-containing protein 11

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Epstein-Barr nuclear antigen 2

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

5hda__assembly_1__model_1

5hda__assembly_1__model_1 | I(q)

5hda__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)