SAXSdb — 2qyf

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

Mitotic spindle assembly checkpoint protein MAD2A

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	MAD2L1-binding protein × 1 （Q15013） peptide × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	MAD2L1-binding protein × 1 （Q15013） peptide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MD2L1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–206； UniProt 1–205 Author chain C； PDBConstruct 2–206； UniProt 1–205

MAD2L1-binding protein

Homo sapiens

UniProt Q15013

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Mitotic spindle assembly checkpoint protein MAD2A × 1 （Q13257） peptide × 1 water × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 3	Mitotic spindle assembly checkpoint protein MAD2A × 1 （Q13257） peptide × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MD2BP_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–240； UniProt 36–274 Author chain D； PDBConstruct 2–240； UniProt 36–274

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	2qyf
Deposition date deposition_date	2007-08-14
Structure title title	Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex
Keywords keywords	PROTEIN-PEPTIDE COMPLEX, MAD2 FAMILY, SPINDLE ASSEMBLY CHECKPOINT, Cell cycle, Cell division, Mitosis, Nucleus, Phosphorylation; CELL CYCLE
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.

2qyf__assembly_1__model_1

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

Download this curve (.dat)

2qyf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2qyf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.63 Å
Rg (electron density)	23.51 Å
Total Rg	24.30 Å
Atom count	3185
Residues	390
Excluded volume	57273 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2qyf__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2qyf__assembly_2__model_1`	trimeric （3）	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	Mitotic spindle assembly checkpoint protein MAD2A
Molecular weight formula_weight	23595.8 kDa
Mutation mutation	L13A
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	6944

GMALQLSREQGITARGSAEIVAEFFSFGINSILYQRGIYPSETFTRVQKYGLTLLVTTDLELIKYLNNVVEQLKDWLYKCSVQKLVVVISNIESGEVLERWQFDIECDKTAKDDSAPREKSQKAIQDEIRSVIRQITATVTFLPLLEVSCSFDLLIYTDKDLVVPEKWEESGPQFITNSEEVRLRSFTTTIHKVNSMVAYKIPVND

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	MAD2L1-binding protein
Molecular weight formula_weight	27687.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MTSSTQEPLNASEAFCPRDCMVPVVFPGPVSQEGCCQFTCELLKHIMYQRQQLPLPYEQLKHFYRKPSPQAEEMLKKKPRATTEVSSRKCQQALAELESVLSHLEDFFARTLVPRVLILLGGNALSPKEFYELDLSLLAPYSVDQSLSTAACLRRLFRAIFMADAFSELQAPPLMGTVVMAQGHRNCGEDWFRPKLNYRVPSRGHKLTVTLSCGRPSIRTTAWEDYIWFQAPVTFKGFRE

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	peptide
Molecular weight formula_weight	1451.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

SWYSYPPPQRAV

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	658

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2qyfa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

Domain ID domain_id	d2qyfc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.135 — The spindle assembly checkpoint protein mad2
Superfamily Superfamily superfamily	d.135.1 — The spindle assembly checkpoint protein mad2
Family Family family	d.135.1.1 — The spindle assembly checkpoint protein mad2

CATH v4.4 (4 domains)

Domain ID domain_id	2qyfA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2qyfB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2qyfC00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	10 — HORMA domain

Domain ID domain_id	2qyfD00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	900 — Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	68.667 Å
Unit-cell length b length_b	104.519 Å
Unit-cell length c length_c	138.825 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	8

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

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1898
R_work r_work	0.1870
R_free r_free	0.2567

Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex

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

Mitotic spindle assembly checkpoint protein MAD2A

State in the Current Structure

Other States of the Same Protein in the Database

MAD2L1-binding protein

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

2qyf__assembly_1__model_1

2qyf__assembly_1__model_1 | I(q)

2qyf__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (4)

Crystal structure of the Mad2/p31(comet)/Mad2-binding peptide ternary complex

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

Mitotic spindle assembly checkpoint protein MAD2A

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

MAD2L1-binding protein

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

2qyf__assembly_1__model_1

2qyf__assembly_1__model_1 | I(q)

2qyf__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

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

7. Citations (4)