SAXSdb — 1ytm

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

phosphoenolpyruvate carboxykinase [ATP]

Anaerobiospirillum succiniciproducens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 OXALIC ACID × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	MAGNESIUM ION × 1 MANGANESE (II) ION × 1 ADENOSINE-5'-TRIPHOSPHATE × 1 OXALIC ACID × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PPCK_ANASU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–532； UniProt 1–532 Author chain B； PDBConstruct 1–532； UniProt 1–532

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	1ytm
Deposition date deposition_date	2005-02-10
Structure title title	Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions
Keywords keywords	kinase; domain closure; nucleotide binding; parallel beta sheet-like hydrogen bond, LYASE; LYASE
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.

1ytm__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1ytm__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1ytm__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	23.40 Å
Rg (electron density)	22.45 Å
Total Rg	23.34 Å
Atom count	4047
Residues	517
Excluded volume	72230 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1ytm__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1ytm__assembly_2__model_1`	monomeric （1）	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 (6)

Entity 1 Entity 1 polymer

Description description	phosphoenolpyruvate carboxykinase [ATP]
Molecular weight formula_weight	58709.6 kDa
EC 编号 ec_number	4.1.1.49
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	8462

MSLSESLAKYGITGATNIVHNPSHEELFAAETQASLEGFEKGTVTEMGAVNVMTGVYTGRSPKDKFIVKNEASKEIWWTSDEFKNDNKPVTEEAWAQLKALAGKELSNKPLYVVDLFCGANENTRLKIRFVMEVAWQAHFVTNMFIRPTEEELKGFEPDFVVLNASKAKVENFKELGLNSETAVVFNLAEKMQIILNTWYGGEMKKGMFSMMNFYLPLQGIAAMHCSANTDLEGKNTAIFFGLSGTGKTTLSTDPKRLLIGDDEHGWDDDGVFNFEGGCYAKVINLSKENEPDIWGAIKRNALLENVTVDANGKVDFADKSVTENTRVSYPIFHIKNIVKPVSKAPAAKRVIFLSADAFGVLPPVSILSKEQTKYYFLSGFTAKLAGTERGITEPTPTFSSCFGAAFLTLPPTKYAEVLVKRMEASGAKAYLVNTGWNGTGKRISIKDTRGIIDAILDGSIDTANTATIPYFNFTVPTELKGVDTKILDPRNTYADASEWEVKAKDLAERFQKNFKKFESLGGDLVKAGPQL

Source Source

Source organism organism	Anaerobiospirillum succiniciproducens
NCBI taxonomy ID ncbi_taxonomy_id	13335
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	2

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 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 5 Entity 5 non-polymer

Description description	OXALIC ACID
Molecular weight formula_weight	90.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	384

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ytma1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.0 — automated matches

Domain ID domain_id	d1ytma2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.0 — automated matches

Domain ID domain_id	d1ytmb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.109 — PEP carboxykinase N-terminal domain
Superfamily Superfamily superfamily	c.109.1 — PEP carboxykinase N-terminal domain
Family Family family	c.109.1.0 — automated matches

Domain ID domain_id	d1ytmb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.91 — PEP carboxykinase-like
Superfamily Superfamily superfamily	c.91.1 — PEP carboxykinase-like
Family Family family	c.91.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	1ytmA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	1ytmA02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	1ytmA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	1ytmB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	449 — Phosphoenolpyruvate Carboxykinase; domain 1
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 1

Domain ID domain_id	1ytmB02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	8 — Phosphoenolpyruvate Carboxykinase; domain 2
Homologous superfamily homologous superfamily	10 — Phosphoenolpyruvate Carboxykinase, domain 2

Domain ID domain_id	1ytmB03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	228 — Phosphoenolpyruvate Carboxykinase; domain 3
Homologous superfamily homologous superfamily	20 —

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Unit-cell length a length_a	194.871 Å
Unit-cell length b length_b	123.219 Å
Unit-cell length c length_c	48.463 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2210
R_work r_work	0.2146
R_free r_free	0.2513

Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions

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

phosphoenolpyruvate carboxykinase [ATP]

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

1ytm__assembly_2__model_1

1ytm__assembly_2__model_1 | I(q)

1ytm__assembly_2__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of phosphoenolpyruvate carboxykinase of Anaerobiospirillum succiniciproducens complexed with ATP, oxalate, magnesium and manganese ions

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

phosphoenolpyruvate carboxykinase [ATP]

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

1ytm__assembly_2__model_1

1ytm__assembly_2__model_1 | I(q)

1ytm__assembly_2__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)