SAXSdb — 1dkd

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

GROEL

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	12-MER PEPTIDE × 1 water × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	12-MER PEPTIDE × 1 water × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	12-MER PEPTIDE × 1 water × 1	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	12-MER PEPTIDE × 1 water × 1	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 4	12-MER PEPTIDE × 2 water × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 4	12-MER PEPTIDE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CH60_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 191–336 Author chain B； PDBConstruct 1–146； UniProt 191–336 Author chain C； PDBConstruct 1–146； UniProt 191–336 Author chain D； PDBConstruct 1–146； UniProt 191–336

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	1dkd
Deposition date deposition_date	1999-12-07
Structure title title	CRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PEPTIDE COMPLEX
Keywords keywords	;MOLECULAR CHAPERON, HSP60, PROTEIN FOLDING, PEPTIDE SELECTION, PHAGE DISPLAY, PEPTIDE BINDING GROOVE FORMED BY PAIRED HELICES SUBSTRATE PEPTIDE IN BETA-SHEET, CHAPERONE ;; 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.

1dkd__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1dkd__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1dkd__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	16.12 Å
Rg (electron density)	14.58 Å
Total Rg	15.85 Å
Atom count	1183
Residues	157
Excluded volume	21470 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1dkd__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1dkd__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1dkd__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1dkd__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1dkd__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1dkd__assembly_6__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 (3)

Entity 1 Entity 1 polymer

Description description	GROEL
Molecular weight formula_weight	15729.3 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4818

EGMQFDRGYLSPYFINKPETGAVELESPFILLADKKISNIREMLPVLEAVAKAGKPLLIIAEDVEGEALATLVVNTMRGIVKVAAVKAPGFGDRRKAMLQDIATLTGGTVISEEIGMELEKATLEDLGQAKRVVINKDTTTIIDGV

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	12-MER PEPTIDE
Molecular weight formula_weight	1460.7 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

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

SWMTTPWGFLHP

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dkda_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.1 — GroEL-like chaperone, apical domain

Domain ID domain_id	d1dkdb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.1 — GroEL-like chaperone, apical domain

Domain ID domain_id	d1dkdc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.1 — GroEL-like chaperone, apical domain

Domain ID domain_id	d1dkdd_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.8 — The 'swivelling' beta/beta/alpha domain
Superfamily Superfamily superfamily	c.8.5 — GroEL apical domain-like
Family Family family	c.8.5.1 — GroEL-like chaperone, apical domain

CATH v4.4 (4 domains)

Domain ID domain_id	1dkdA00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1dkdB00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1dkdC00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

Domain ID domain_id	1dkdD00
Class class	3 — Alpha Beta
Architecture architecture	50 — 3-Layer(bba) Sandwich
Topology topology	7 — GroEL
Homologous superfamily homologous superfamily	10 — GroEL

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Unit-cell length a length_a	42.042 Å
Unit-cell length b length_b	134.668 Å
Unit-cell length c length_c	59.734 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.38 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2150
R_free r_free	0.2640

CRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PEPTIDE COMPLEX

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

GROEL

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

1dkd__assembly_4__model_1

1dkd__assembly_4__model_1 | I(q)

1dkd__assembly_4__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A GROEL (APICAL DOMAIN) AND A DODECAMERIC PEPTIDE COMPLEX

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

GROEL

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

1dkd__assembly_4__model_1

1dkd__assembly_4__model_1 | I(q)

1dkd__assembly_4__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) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)