SAXSdb — 1pdk

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

PROTEIN (CHAPERONE PROTEIN PAPD)

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (PROTEIN PAPK) × 1 （P62532） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAPD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–218； UniProt 22–239

PROTEIN (PROTEIN PAPK)

OrganismNot specified

UniProt P62532

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	PROTEIN (CHAPERONE PROTEIN PAPD) × 1 （P15319） water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PAPK_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–157； UniProt 22–178

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	1pdk
Deposition date deposition_date	1999-03-29
Structure title title	PAPD-PAPK CHAPERONE-PILUS SUBUNIT COMPLEX FROM E.COLI P PILUS
Keywords keywords	CHAPERONE, PILUS, BACTERIAL ADHESION; CHAPERONE
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.

1pdk__assembly_1__model_1

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

Download this curve (.dat)

1pdk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1pdk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.74 Å
Rg (electron density)	22.95 Å
Total Rg	23.71 Å
Atom count	2803
Residues	364
Excluded volume	49871 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1pdk__assembly_1__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	PROTEIN (CHAPERONE PROTEIN PAPD)
Molecular weight formula_weight	24589.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2903

AVSLDRTRAVFDGSEKSMTLDISNDNKQLPYLAQAWIENENQEKIITGPVIATPPVQRLEPGAKSMVRLSTTPDISKLPQDRESLFYFNLREIPPRSEKANVLQIALQTKIKLFYRPAAIKTRPNEVWQDQLILNKVSGGYRIENPTPYYVTVIGLGGSEKQAEEGEFETVMLSPRSEQTVKSANYNTPYLSYINDYGGRPVLSFICNGSRCSVKKEK

Entity 2 Entity 2 polymer

Description description	PROTEIN (PROTEIN PAPK)
Molecular weight formula_weight	16865.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SDVAFRGNLLDRPCHVSGDSLNKHVVFKTRASRDFWYPPGRSPTESFVIRLENCHATAVGKIVTLTFKGTEEAALPGHLKVTGVNAGRLGIALLDTDGSSLLKPGTSHNKGQGEKVTGNSLELPFGAYVVATPEALRTKSVVPGDYEATATFELTYR

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	100

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1pdka1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.11 — PapD-like
Family Family family	b.1.11.1 — Pilus chaperone

Domain ID domain_id	d1pdka2
Class class	b — All beta proteins
Fold Fold fold	b.7 — C2 domain-like
Superfamily Superfamily superfamily	b.7.2 — Periplasmic chaperone C-domain
Family Family family	b.7.2.1 — Periplasmic chaperone C-domain

Domain ID domain_id	d1pdkb_
Class class	b — All beta proteins
Fold Fold fold	b.2 — Common fold of diphtheria toxin/transcription factors/cytochrome f
Superfamily Superfamily superfamily	b.2.3 — Bacterial adhesins
Family Family family	b.2.3.2 — Pilus subunits

CATH v4.4 (3 domains)

Domain ID domain_id	1pdkA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1pdkA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	1pdkB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1090 — Fimbrial-type adhesion domain

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Unit-cell length a length_a	62.120 Å
Unit-cell length b length_b	63.690 Å
Unit-cell length c length_c	92.720 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	4

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

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2350
R_free r_free	0.2730

PAPD-PAPK CHAPERONE-PILUS SUBUNIT COMPLEX FROM E.COLI P PILUS

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

PROTEIN (CHAPERONE PROTEIN PAPD)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (PROTEIN PAPK)

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

1pdk__assembly_1__model_1

1pdk__assembly_1__model_1 | I(q)

1pdk__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

PAPD-PAPK CHAPERONE-PILUS SUBUNIT COMPLEX FROM E.COLI P PILUS

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

PROTEIN (CHAPERONE PROTEIN PAPD)

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

PROTEIN (PROTEIN PAPK)

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

1pdk__assembly_1__model_1

1pdk__assembly_1__model_1 | I(q)

1pdk__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

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)