SAXSdb — 5kbx

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

Phosphorelay intermediate protein YPD1

Saccharomyces cerevisiae S288C

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Osmolarity two-component system protein SSK1 × 1 （Q07084） GLYCEROL × 3 PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YPD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–167； UniProt 1–167

Osmolarity two-component system protein SSK1

Saccharomyces cerevisiae S288C

UniProt Q07084

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Phosphorelay intermediate protein YPD1 × 1 （Q07688） GLYCEROL × 3 PHOSPHATE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SSK1_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–218； UniProt 495–712

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	5kbx
Deposition date deposition_date	2016-06-03
Structure title title	Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1
Keywords keywords	;two-component signaling, phosphorelay, Ypd1, Ssk1, response regulator, histidine phosphotransfer protein, Saccharomyces cerevisiae, co-crystal, phosphotransfer, SIGNALING PROTEIN ;; SIGNALING 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.

5kbx__assembly_1__model_1

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

Download this curve (.dat)

5kbx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5kbx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.10 Å
Rg (electron density)	21.27 Å
Total Rg	22.19 Å
Atom count	2396
Residues	294
Excluded volume	43104 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5kbx__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 (5)

Entity 1 Entity 1 polymer

Description description	Phosphorelay intermediate protein YPD1
Molecular weight formula_weight	19187.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2435

MSTIPSEIINWTILNEIISMDDDDSDFSKGLIIQFIDQAQTTFAQMQRQLDGEKNLTELDNLGHFLKGSSAALGLQRIAWVCERIQNLGRKMEHFFPNKTELVNTLSDKSIINGINIDEDDEEIKIQVDDKDENSIYLILIAKALNQSRLEFKLARIELSKYYNTNL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli DH5[alpha]

Entity 2 Entity 2 polymer

Description description	Osmolarity two-component system protein SSK1
Molecular weight formula_weight	24457.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TTSEKVFPKINVLIVEDNVINQAILGSFLRKHKISYKLAKNGQEAVNIWKEGGLHLIFMDLQLPVLSGIEAAKQIRDFEKQNGIGIQKSLNNSHSNLEKGTSKRFSQAPVIIVALTASNSQMDKRKALLSGCNDYLTKPVNLHALSKKITEWGCMQALIDFDSWKQGESRMTDSVLVKSPQKPIAPSNPHSFKQATSMTPTHSPVRKNSNLSPTQIEL

Source Source

Source organism organism	Saccharomyces cerevisiae S288C
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	30

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6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5kbxa_
Class class	a — All alpha proteins
Fold Fold fold	a.24 — Four-helical up-and-down bundle
Superfamily Superfamily superfamily	a.24.10 — Histidine-containing phosphotransfer domain, HPT domain
Family Family family	a.24.10.2 — Phosphorelay protein-like

Domain ID domain_id	d5kbxb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.23 — Flavodoxin-like
Superfamily Superfamily superfamily	c.23.1 — CheY-like
Family Family family	c.23.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	5kbxA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	160 — HPT domain

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Unit-cell length a length_a	71.696 Å
Unit-cell length b length_b	71.696 Å
Unit-cell length c length_c	176.389 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	33.270 Å
R factor r_factor	0.2325
R_work r_work	0.2275
R_free r_free	0.2785

Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1

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

Phosphorelay intermediate protein YPD1

State in the Current Structure

Other States of the Same Protein in the Database

Osmolarity two-component system protein SSK1

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

5kbx__assembly_1__model_1

5kbx__assembly_1__model_1 | I(q)

5kbx__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (3)

Co-crystal structure of the Saccharomyces cerevisiae histidine phosphotransfer signaling protein Ypd1 and the receiver domain of its downstream response regulator Ssk1

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

Phosphorelay intermediate protein YPD1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Osmolarity two-component system protein SSK1

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

5kbx__assembly_1__model_1

5kbx__assembly_1__model_1 | I(q)

5kbx__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (3)