SAXSdb — 1k3d

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

Phosphoenolpyruvate carboxykinase

Escherichia coli

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–540	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.8；294 K；ADP, Aluminum Nitrate, Magnesium Chloride, Sodium Fluoride, EDTA, ammonium acetate, sodium acetate buffer, dithiothreitol, PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.00 Å R-free 0.266

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1K3D	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11KO Structure of Escherichia coli phosphoenolpyruvate carboxykinase with bound ATP, Mg2+, and Mn2+ Deposited 2026-03-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–540（539 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；4 ul drop with 4 mg/mL protein, 1 mM ADP, 1 mM phosphoenol pyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.5), 200 mM ammonium acetate and 12% PEG 4000 was allowed to equilibrate with a 1 mL reservoir of 100 mM sodium acetate, 200 mM ammonium acetate and 31% PEG 4000	Resolution 1.58 Å R-free 0.185
1AQ2 PHOSPHOENOLPYRUVATE CARBOXYKINASE Deposited 1997-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	MN MANGANESE (II) ION × 1 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 PYR PYRUVIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.4；pH 4.4	Resolution 1.90 Å R-free 0.260
1AYL PHOSPHOENOLPYRUVATE CARBOXYKINASE Deposited 1995-12-07	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	OXL OXALATE ION × 1 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.234
1K3C Phosphoenolpyruvate carboxykinase in complex with ADP, AlF3 and Pyruvate Deposited 2001-10-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 PYR PYRUVIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；294 K；ADP, Aluminum Nitrate, Magnesium Chloride, Sodium Fluoride, Pyruvate, EDTA, ammonium acetate, sodium acetate buffer, dithiothreitol, PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K	Resolution 2.00 Å R-free 0.285
1OEN PHOSPHOENOLPYRUVATE CARBOXYKINASE Deposited 1995-09-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å R-free 0.244
1OS1 Structure of Phosphoenolpyruvate Carboxykinase complexed with ATP,Mg, Ca and pyruvate. Deposited 2003-03-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 PYR PYRUVIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；294 K；ADP, Calcium Chloride, Magnesium Chloride, PEP, EDTA, ammonium acetate, sodium acetate buffer, dithiothreitol, PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 1.80 Å R-free 0.250
2OLQ How Does an Enzyme Recognize CO2? Deposited 2007-01-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	MN MANGANESE (II) ION × 1 MG MAGNESIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CO2 CARBON DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 4.5；298 K；30% P4000, 0.1 M sodium acetate pH 4.5, 0.2 M ammonium acetate, VAPOR DIFFUSION, temperature 298K	Resolution 1.94 Å R-free 0.235
2OLR Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase complexed with carbon dioxide, Mg2+, ATP Deposited 2007-01-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 CO2 CARBON DIOXIDE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；293 K；8 microL drops: 8 mg/ml protein concentration, 2 mM ATP, 5 mM oxalate, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate, 12% PEG 4000, 1 ml resevoir: 100 mM sodium acetate, 200 mM ammonuim acetate, 27% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.198
2PXZ E. coli phosphoenolpyruvate carboxykinase (PEPCK) complexed with ATP, Mg2+, Mn2+, carbon dioxide and oxaloacetate Deposited 2007-05-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–540（540 aa）	Not recorded	MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 OAA OXALOACETATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CO2 CARBON DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.4；294 K；8ul drop with 8ug/ml protein, 2mM ADP, 5mM MgCl2, 10 uM MnCl2, 1 mM EDTA, 100 mM sodium acetate (pH 4.4), 200 mM ammonium acetate and 12% w/v PEG 4000 was allowed to equilibrate with a 1 ml reservoir of 100 mM sodium aceate, 200 mM ammonium acetate and 27% PEG 4000. After crystals grew for one week 2ul of a 1 mM EDTA and saturated sodium oxaloacetate solution was added to the drop. 5 ul of glycerol was added to the drop. A 0.1 x 0.1 x 0.3 mm crystal was removed with a loop and flash cooled in liquid nitrogen, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.23 Å R-free 0.234
2PY7 Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys213Ser complexed with ATP-Mg2+-Mn2+ Deposited 2007-05-15	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1–540（540 aa）	Mutation：K213S	MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；A 2ul drop with 4 mg/ml protein, 20 mM Tris-HCl (pH 7.6), 0.5 mM EDTA, 5 mM ADP, 2.5 mM phosphoenolpyruvate, 2.5 mM MgCl2, 2.5 mM MnCl2, 0.1 M sodium acetate, 0.05 M sodium cacodylate (pH 6.5), 15% PEG 8000 was allowed to equilibrate with a 1 ml well of 0.2 M sodium aceate, 0.1 M sodium cacodylate 30% PEG 8000. After a week a 0.1 x 0.1 x 0.4 mm crystal was removed and put in a small volume of well solution with 30% glycerol added. The crystal was put into a loop and flash cooled in liquid notrogen, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.218
6ASI E. coli phosphoenolpyruvate carboxykinase G209S mutant bound to methanesulfonate Deposited 2017-08-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Mutation：G209S	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 03S methanesulfonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；16% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.3 M sodium chloride, 0.1 M sodium methanesulfonate	Resolution 1.79 Å R-free 0.185
6ASM E. coli phosphoenolpyruvate carboxykinase G209S K212C mutant bound to thiosulfate Deposited 2017-08-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Mutation：G209S, K212C	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 MN MANGANESE (II) ION × 1 XE XENON × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 THJ THIOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.1 M Bis-Tris pH 5.5, 0.4 M sodium chloride	Resolution 1.55 Å R-free 0.188
6ASN E. coli phosphoenolpyruvate carboxykinase K212I F216V mutant bound to methanesulfonate Deposited 2017-08-25	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Mutation：K212I, F216V	SO4 SULFATE ION × 3 03S methanesulfonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.16 M ammonium sulfate, 0.08 M sodium acetate pH 4.8, 20% PEG 4000, 15% v/v glycerol	Resolution 1.55 Å R-free 0.193
6AT2 E. coli phosphoenolpyruvate carboxykinase G209N mutant bound to thiosulfate Deposited 2017-08-27	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Mutation：G209N	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 MG MAGNESIUM ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 THJ THIOSULFATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；24% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate	Resolution 1.44 Å R-free 0.191
6AT3 E. coli phosphoenolpyruvate carboxykinase Y207F mutant bound to thiosulfate and oxaloacetate Deposited 2017-08-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–540（540 aa） Chain B 1–540（540 aa）	Mutation：Y207F Mutation：Y207F	OAA OXALOACETATE ION × 1 THJ THIOSULFATE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；24% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate	Resolution 1.46 Å R-free 0.219
6AT4 E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate Deposited 2017-08-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Not recorded	THJ THIOSULFATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate	Resolution 1.33 Å R-free 0.151
6AT4 E. coli phosphoenolpyruvate carboxykinase bound to thiosulfate Deposited 2017-08-27	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–540（540 aa）	Not recorded	THJ THIOSULFATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.4 M sodium chloride, 0.1 M Bis-Tris pH 5.5, 0.1 M sodium thiosulfate	Resolution 1.33 Å R-free 0.151
6COM 2.3A crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Asp269Asn Deposited 2018-03-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–540（540 aa）	Mutation：D269N	ATP ADENOSINE-5'-TRIPHOSPHATE × 1 PYR PYRUVIC ACID × 1 CA CALCIUM ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.2；293 K；A 2ul drop with 2 mg/ml protein, 5 mM Calcium chloride, 5mM Magnesium chloride, 2 mM ATP, 2mM Pyruvate, 1 mM EDTA, 200 mM Ammonium acetate, 100 mM Sodium acetate, 0.01 mM DTT, 30% PEG 4000 was added to 2 ul drop containing 2 M sodium aceate, 0.1 M Tris pH 8.2 30% PEG 4000. After a week a rod like crystal was removed and soaked in a solution with 30% glycerol 1mM EDTA, 100 mM sodium acetate 200mM ammonium acetate and 12% PEG 4000. The crystal was put into a loop and flash cooled in liquid notrogen	Resolution 2.30 Å R-free 0.209

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPCK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–540； UniProt 1–540

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	1k3d
Deposition date deposition_date	2001-10-02
Structure title title	Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3
Keywords keywords	Kinase, gluconeogenesis, nucleotide-triphosphate hydrolase., LYASE; LYASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	24.13 Å
Radius of gyration Rg (electron density) rg_electron	23.06 Å
Forward intensity I(0) i0	57851200.00
Molecular weight molecular_weight	59016.0 kDa
Excluded volume excluded_volume	73659 Å³
Envelope volume envelope_volume	84713 Å³
Hydration-shell volume shell_volume	29708 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	30.96 Å
Envelope Rg envelope_rg	23.24 Å
Shape Rg shape_rg	23.07 Å
Total Rg total_rg	23.89 Å
Total atoms total_atoms	4159
Residues n_residues	535
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.8 Å
Rg (real space) rg_real	24.02 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	5.7850e+07
I(0) uncertainty (real space) i0_real_error	8.4730e+05
Rg (reciprocal space) rg_reciprocal	24.05 Å
I(0) (reciprocal space) i0_reciprocal	57850000.0000
Solution quality estimate total_estimate	0.6103
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.249
Kurtosis Kurtosis kurtosis	-0.337
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19410000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.776; Stabil: 0.998; Sysdev: 0.203; Positv: 1.000; Valcen: 0.999; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Phosphoenolpyruvate carboxykinase
Molecular weight formula_weight	59709.2 kDa
EC 编号 ec_number	4.1.1.49
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	4434

MRVNNGLTPQELEAYGISDVHDIVYNPSYDLLYQEELDPSLTGYERGVLTNLGAVAVDTGIFTGRSPKDKYIVRDDTTRDTFWWADKGKGKNDNKPLSPETWQHLKGLVTRQLSGKRLFVVDAFCGANPDTRLSVRFITEVAWQAHFVKNMFIRPSDEELAGFKPDFIVMNGAKCTNPQWKEQGLNSENFVAFNLTERMQLIGGTWYGGEMKKGMFSMMNYLLPLKGIASMHCSANVGEKGDVAVFFGLSGTGKTTLSTDPKRRLIGDDEHGWDDDGVFNFEGGCYAKTIKLSKEAEPEIYNAIRRDALLENVTVREDGTIDFDDGSKTENTRVSYPIYHIDNIVKPVSKAGHATKVIFLTADAFGVLPPVSRLTADQTQYHFLSGFTAKLAGTERGITEPTPTFSACFGAAFLSLHPTQYAEVLVKRMQAAGAQAYLVNTGWNGTGKRISIKDTRAIIDAILNGSLDNAETFTLPMFNLAIPTELPGVDTKILDPRNTYASPEQWQEKAETLAKLFIDNFDKYTDTPAGAALVAAGPKL

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	562
宿主生物 host_organism	Escherichia coli K12

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	1

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	275

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1k3da1
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.91.1.1 — PEP carboxykinase C-terminal domain

Domain ID domain_id	d1k3da2
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.109.1.1 — PEP carboxykinase N-terminal domain

CATH v4.4 (3 domains)

Domain ID domain_id	1k3dA01
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	1k3dA02
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	1k3dA03
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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8. Citations (1)

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Unit-cell length a length_a	126.033 Å
Unit-cell length b length_b	95.844 Å
Unit-cell length c length_c	46.608 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.59 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1980
R_work r_work	0.1960
R_free r_free	0.2660

fit	/app/data/saxs_computation/k3/1k3d/1k3d.fit
pddf	/app/data/pr_computation/k3/1k3d/1k3d.pr.out
profile	/app/data/saxs_computation/k3/1k3d/1k3d.dat

Phosphoenolpyruvate carboxykinase in complex with ADP and AlF3

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

Phosphoenolpyruvate carboxykinase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction