1poy

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)

Method: X-RAY DIFFRACTION

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

SPERMIDINE/PUTRESCINE-BINDING PROTEIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SPERMIDINE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	SPERMIDINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	POTD_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–323； UniProt 26–348 Author chain 2； PDBConstruct 1–323； UniProt 26–348 Author chain 3； PDBConstruct 1–323； UniProt 26–348 Author chain 4； PDBConstruct 1–323； UniProt 26–348

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	1poy
Deposition date deposition_date	1996-02-02
Structure title title	SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)
Keywords keywords	TRANSPORT PROTEIN, BINDING PROTEIN; TRANSPORT 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.

1poy__assembly_1__model_1

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

Download this curve (.dat)

1poy__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1poy__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.09 Å
Rg (electron density)	25.09 Å
Total Rg	26.07 Å
Atom count	5137
Residues	646
Excluded volume	91775 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1poy__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1poy__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	SPERMIDINE/PUTRESCINE-BINDING PROTEIN
Molecular weight formula_weight	36297.9 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3,4
Atom count atom_count	10512

NNTLYFYNWTEYVPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDLVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPEYKGSLLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNSDNPANPYMEGEVNLGMIWNGSAFVARQAGTPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLLRPDVAKQVAETIGYPTPNLAARKLLSPEVANDKTLYPDAETIKNGEWQNDVGAASSIYEEYYQKLKAGR

Entity 2 Entity 2 non-polymer

Description description	SPERMIDINE
Molecular weight formula_weight	145.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	235

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1poy1_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d1poy2_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d1poy3_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

Domain ID domain_id	d1poy4_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.94 — Periplasmic binding protein-like II
Superfamily Superfamily superfamily	c.94.1 — Periplasmic binding protein-like II
Family Family family	c.94.1.1 — Phosphate binding protein-like

CATH v4.4 (8 domains)

Domain ID domain_id	1poy101
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy102
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy201
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy202
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy301
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy302
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy401
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

Domain ID domain_id	1poy402
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	190 — D-Maltodextrin-Binding Protein; domain 2
Homologous superfamily homologous superfamily	10 — Periplasmic binding protein-like II

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Unit-cell length a length_a	145.300 Å
Unit-cell length b length_b	69.100 Å
Unit-cell length c length_c	72.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.60 °
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	2.500 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1990
R_work r_work	0.1990
R_free r_free	0.2800

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)

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

SPERMIDINE/PUTRESCINE-BINDING PROTEIN

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

1poy__assembly_1__model_1

1poy__assembly_1__model_1 | I(q)

1poy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (3)

SPERMIDINE/PUTRESCINE-BINDING PROTEIN COMPLEXED WITH SPERMIDINE (DIMER FORM)

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

SPERMIDINE/PUTRESCINE-BINDING 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1poy__assembly_1__model_1

1poy__assembly_1__model_1 | I(q)

1poy__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (3)