SAXSdb — 5k4f

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

Golgi-associated PDZ and coiled-coil motif-containing protein

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	HPV18E6 peptide × 1 （P06463） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	HPV18E6 peptide × 1 （P06463） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GOPC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–87； UniProt 284–370 Author chain B； PDBConstruct 1–87； UniProt 284–370

HPV18E6 peptide

OrganismNot specified

UniProt P06463

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Golgi-associated PDZ and coiled-coil motif-containing protein × 1 （Q9HD26） water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Golgi-associated PDZ and coiled-coil motif-containing protein × 1 （Q9HD26） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	VE6_HPV18
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–10； UniProt 149–158 Author chain D； PDBConstruct 1–10； UniProt 149–158

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	5k4f
Deposition date deposition_date	2016-05-20
Structure title title	CAL PDZ mutant C319A with a peptide
Keywords keywords	CAL PDZ mutant, C319A, PEPTIDE BINDING PROTEIN; PEPTIDE BINDING PROTEIN
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.

5k4f__assembly_1__model_1

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

Download this curve (.dat)

5k4f__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5k4f__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	13.66 Å
Rg (electron density)	12.10 Å
Total Rg	13.47 Å
Atom count	712
Residues	93
Excluded volume	12666 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5k4f__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5k4f__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 (3)

Entity 1 Entity 1 polymer

Description description	Golgi-associated PDZ and coiled-coil motif-containing protein
Molecular weight formula_weight	9321.7 kDa
Mutation mutation	C319A
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	1750

GPIRKVLLLKEDHEGLGISITGGKEHGVPILISEIHPGQPADRAGGLHVGDAILAVNGVNLRDTKHKEAVTILSQQRGEIEFEVVYV

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	HPV18E6 peptide
Molecular weight formula_weight	1345.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

RLQRRRETQV

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	143

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5k4fA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	5k4fB00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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Unit-cell length a length_a	32.730 Å
Unit-cell length b length_b	48.276 Å
Unit-cell length c length_c	51.435 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	101.76 °
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	1.360 Å
Low-resolution limit resolution_low	18.791 Å
R factor r_factor	0.1552
R_work r_work	0.1536
R_free r_free	0.1833

CAL PDZ mutant C319A with a peptide

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

Golgi-associated PDZ and coiled-coil motif-containing protein

State in the Current Structure

Other States of the Same Protein in the Database

HPV18E6 peptide

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

5k4f__assembly_1__model_1

5k4f__assembly_1__model_1 | I(q)

5k4f__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

CAL PDZ mutant C319A with a peptide

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

Golgi-associated PDZ and coiled-coil motif-containing 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

HPV18E6 peptide

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

5k4f__assembly_1__model_1

5k4f__assembly_1__model_1 | I(q)

5k4f__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)