1xdp

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

Method: X-RAY DIFFRACTION

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

Polyphosphate kinase

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 4 ADENOSINE-5'-TRIPHOSPHATE × 2 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	MAGNESIUM ION × 8 ADENOSINE-5'-TRIPHOSPHATE × 4 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–687； UniProt 1–687 Author chain B； PDBConstruct 1–687； UniProt 1–687

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	1xdp
Deposition date deposition_date	2004-09-07
Structure title title	Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP
Keywords keywords	E.coli polyphosphate kinase, PPK, PPK complex with AMPPNP, AMPPNP, TRANSFERASE; TRANSFERASE
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.

1xdp__assembly_1__model_1

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

Download this curve (.dat)

1xdp__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1xdp__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.43 Å
Rg (electron density)	36.50 Å
Total Rg	37.07 Å
Atom count	11408
Residues	1374
Excluded volume	203430 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1xdp__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1xdp__assembly_2__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 (4)

Entity 1 Entity 1 polymer

Description description	Polyphosphate kinase
Molecular weight formula_weight	80414.2 kDa
EC 编号 ec_number	2.7.4.1
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	11538

GQEKLYIEKELSWLSFNERVLQEAADKSNPLIERMRFLGIYSNNLDEFYKVRFAELKRRIIISEEQGSNSHSRHLLGKIQSRVLKADQEFDGLYNELLLEMARNQIFLINERQLSVNQQNWLRHYFKQYLRQHITPILINPDTDLVQFLKDDYTYLAVEIIRGDTIRYALLEIPSDKVPRFVNLPPEAPRRRKPMILLDNILRYCLDDIFKGFFDYDALNAYSMKMTRDAEYDLVHEMEASLMELMSSSLKQRLTAEPVRFVYQRDMPNALVEVLREKLTISRYDSIVPGGRYHNFKDFINFPNVGKANLVNKPLPRLRHIWFDKAQFRNGFDAIRERDVLLYYPYHTFEHVLELLRQASFDPSVLAIKINIYRVAKDSRIIDSMIHAAHNGKKVTVVVELQARFDEEANIHWAKRLTEAGVHVIFSAPGLKIHAKLFLISRKENGEVVRYAHIGTGNFNEKTARLYTDYSLLTADARITNEVRRVFNFIENPYRPVTFDYLMVSPQNSRRLLYEMVDREIANAQQGLPSGITLKLNNLVDKGLVDRLYAASSSGVPVNLLVRGMCSLIPNLEGISDNIRAISIVDRYLEHDRVYIFENGGDKKVYLSSADWMTRNIDYRIEVATPLLDPRLKQRVLDIIDILFSDTVKARYIDKELSNRYVPRGNRRKVRAQLAIYDYIKSLEQPE

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1xdpa1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.15 — PPK N-terminal domain-like
Family Family family	a.7.15.1 — PPK N-terminal domain-like

Domain ID domain_id	d1xdpa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.322 — PHP14-like
Superfamily Superfamily superfamily	d.322.1 — PHP14-like
Family Family family	d.322.1.2 — PPK middle domain-like

Domain ID domain_id	d1xdpa3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

Domain ID domain_id	d1xdpa4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

Domain ID domain_id	d1xdpb1
Class class	a — All alpha proteins
Fold Fold fold	a.7 — Spectrin repeat-like
Superfamily Superfamily superfamily	a.7.15 — PPK N-terminal domain-like
Family Family family	a.7.15.1 — PPK N-terminal domain-like

Domain ID domain_id	d1xdpb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.322 — PHP14-like
Superfamily Superfamily superfamily	d.322.1 — PHP14-like
Family Family family	d.322.1.2 — PPK middle domain-like

Domain ID domain_id	d1xdpb3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

Domain ID domain_id	d1xdpb4
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.136 — Phospholipase D/nuclease
Superfamily Superfamily superfamily	d.136.1 — Phospholipase D/nuclease
Family Family family	d.136.1.4 — Polyphosphate kinase C-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id	1xdpA01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	310 — Polyphosphate kinase N-terminal domain

Domain ID domain_id	1xdpA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1840 — polyphosphate kinase like
Homologous superfamily homologous superfamily	10 — Polyphosphate kinase middle domain

Domain ID domain_id	1xdpA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	1xdpA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	1xdpB01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily	310 — Polyphosphate kinase N-terminal domain

Domain ID domain_id	1xdpB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1840 — polyphosphate kinase like
Homologous superfamily homologous superfamily	10 — Polyphosphate kinase middle domain

Domain ID domain_id	1xdpB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

Domain ID domain_id	1xdpB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	870 — Endonuclease; Chain A
Homologous superfamily homologous superfamily	10 — Endonuclease Chain A

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Unit-cell length a length_a	152.000 Å
Unit-cell length b length_b	152.000 Å
Unit-cell length c length_c	150.000 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	16

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.3370
R_work r_work	0.2480
R_free r_free	0.2740

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

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

Polyphosphate kinase

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

1xdp__assembly_1__model_1

1xdp__assembly_1__model_1 | I(q)

1xdp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of the E.coli Polyphosphate Kinase in complex with AMPPNP

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

Polyphosphate kinase

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

1xdp__assembly_1__model_1

1xdp__assembly_1__model_1 | I(q)

1xdp__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)