SAXSdb — 8rbh

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

Kelch-like protein 12

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Peflin × 1 （Q9UBV8） 1,2-ETHANEDIOL × 1 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Peflin × 1 （Q9UBV8） SODIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KLH12_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–301； UniProt 268–567 Author chain B； PDBConstruct 2–301； UniProt 268–567

Peflin

OrganismNot specified

UniProt Q9UBV8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Kelch-like protein 12 × 1 （Q53G59） 1,2-ETHANEDIOL × 1 SODIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Kelch-like protein 12 × 1 （Q53G59） SODIUM ION × 3 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PEF1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–11； UniProt 15–25 Author chain D； PDBConstruct 1–11； UniProt 15–25

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	8rbh
Deposition date deposition_date	2023-12-04
Last revision last_revision	2024-12-11
Structure title title	Crystal structure of the kelch domain of human KLHL12 in complex with PEF1 peptide
Keywords keywords	E3 ligase, protein binding, peptide binding, Kelch-like protein, kelch like family member 12., 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.

8rbh__assembly_1__model_1

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

Download this curve (.dat)

8rbh__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8rbh__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.65 Å
Rg (electron density)	17.44 Å
Total Rg	18.36 Å
Atom count	2226
Residues	296
Excluded volume	39115 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8rbh__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8rbh__assembly_2__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	Kelch-like protein 12
Molecular weight formula_weight	32905.9 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	4803

SMQGPRTRARLGANEVLLVVGGFGSQQSPIDVVEKYDPKTQEWSFLPSITRKRRYVASVSLHDRIYVIGGYDGRSRLSSVECLDYTADEDGVWYSVAPMNVRRGLAGATTLGDMIYVSGGFDGSRRHTSMERYDPNIDQWSMLGDMQTAREGAGLVVASGVIYCLGGYDGLNILNSVEKYDPHTGHWTNVTPMATKRSGAGVALLNDHIYVVGGFDGTAHLSSVEAYNIRTDSWTTVTSMTTPRCYVGATVLRGRLYAIAGYDGNSLLSSIECYDPIIDSWEVVTSMGTQRCDAGVCVLRE

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	Peflin
Molecular weight formula_weight	1001.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

GQAPGAPPGSY

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
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	348

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Unit-cell length a length_a	45.001 Å
Unit-cell length b length_b	78.390 Å
Unit-cell length c length_c	73.784 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	99.24 °
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	monoclinic

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	72.830 Å
R factor r_factor	0.2120
R_work r_work	0.2096
R_free r_free	0.2576

Crystal structure of the kelch domain of human KLHL12 in complex with PEF1 peptide

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

Kelch-like protein 12

State in the Current Structure

Other States of the Same Protein in the Database

Peflin

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

8rbh__assembly_1__model_1

8rbh__assembly_1__model_1 | I(q)

8rbh__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of the kelch domain of human KLHL12 in complex with PEF1 peptide

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

Kelch-like protein 12

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Peflin

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

8rbh__assembly_1__model_1

8rbh__assembly_1__model_1 | I(q)

8rbh__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 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)