SAXSdb — 1kdp

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

CYTIDYLATE KINASE

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 1–227	Not recorded	SO4 SULFATE ION × 1 DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.30 Å R-free 0.255
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–227	Not recorded	SO4 SULFATE ION × 1 DCM 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.30 Å R-free 0.255

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 1KDP	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CKE CMP KINASE FROM ESCHERICHIA COLI FREE ENZYME STRUCTURE Deposited 1998-09-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 1.75 Å R-free 0.259
1KDO CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH CYTIDINE MONOPHOSPHATE Deposited 2001-11-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 3 C5P CYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 1.90 Å R-free 0.248
1KDO CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH CYTIDINE MONOPHOSPHATE Deposited 2001-11-13	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 2 C5P CYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 1.90 Å R-free 0.248
1KDR CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH ARA-CYTIDINE MONOPHOSPHATE Deposited 2001-11-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 1 CAR CYTOSINE ARABINOSE-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.25 Å R-free 0.254
1KDR CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH ARA-CYTIDINE MONOPHOSPHATE Deposited 2001-11-13	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 2 CAR CYTOSINE ARABINOSE-5'-PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 2.25 Å R-free 0.254
1KDT CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH 2',3'-DIDEOXY-CYTIDINE MONOPHOSPHATE Deposited 2001-11-13	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 2 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 1.95 Å R-free 0.253
1KDT CYTIDINE MONOPHOSPHATE KINASE FROM E.COLI IN COMPLEX WITH 2',3'-DIDEOXY-CYTIDINE MONOPHOSPHATE Deposited 2001-11-13	Different ligand/ion Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–227（227 aa）	Not recorded	SO4 SULFATE ION × 1 DOC 2',3'-DIDEOXYCYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Ammonium Sulphate, TRIS-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 293K	Resolution 1.95 Å R-free 0.253
2CMK CYTIDINE MONOPHOSPHATE KINASE IN COMPLEX WITH CYTIDINE-DI-PHOSPHATE Deposited 1998-09-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–227（227 aa） Fragment：DOMAIN	Not recorded	SO4 SULFATE ION × 2 CDP CYTIDINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.4；pH 7.4	Resolution 2.00 Å R-free 0.220
2FEM Mutant R188M of the Cytidine Monophosphate Kinase From E. Coli Deposited 2005-12-16	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 1–227（227 aa）	Mutation：R188M	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；Tris-HCL 50 mM pH 7.4, ammonium sulfate 1.3 M, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.242
2FEO Mutant R188M of The Cytidine Monophosphate Kinase from E. coli complexed with dCMP Deposited 2005-12-16	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 1–227（227 aa）	Mutation：R188M	SO4 SULFATE ION × 1 DC 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；dCMP 200 mM, Tris-HCL 50 mM pH 7.4, ammonium sulfate 1.7 M, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.339

7 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KCY_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–227； UniProt 1–227 Author chain B； PDBConstruct 1–227； UniProt 1–227

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	1kdp
Deposition date deposition_date	2001-11-13
Structure title title	CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE
Keywords keywords	NUCLEOTIDE MONOPHOSPHATE KINASE, TRANSFERASE; TRANSFERASE
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	38.20 Å
Radius of gyration Rg (electron density) rg_electron	38.24 Å
Forward intensity I(0) i0	38317600.00
Molecular weight molecular_weight	49013.0 kDa
Excluded volume excluded_volume	61055 Å³
Envelope volume envelope_volume	91882 Å³
Hydration-shell volume shell_volume	19810 Å³
Envelope diameter envelope_diameter	113.0 Å
Shell Rg shell_rg	45.79 Å
Envelope Rg envelope_rg	36.11 Å
Shape Rg shape_rg	38.26 Å
Total Rg total_rg	38.65 Å
Total atoms total_atoms	3446
Residues n_residues	446
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	113.7 Å
Rg (real space) rg_real	38.60 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	3.8320e+07
I(0) uncertainty (real space) i0_real_error	6.3530e+05
Rg (reciprocal space) rg_reciprocal	38.37 Å
I(0) (reciprocal space) i0_reciprocal	38310000.0000
Solution quality estimate total_estimate	0.5781
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.2 Å
Skewness Skewness skewness	0.142
Kurtosis Kurtosis kurtosis	-1.436
Angular range angular_range	— – 0.2050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4475000.0000
Real-space data points n_real_points	42
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.014; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.127; Smooth: 0.344

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	CYTIDYLATE KINASE
Molecular weight formula_weight	24778.3 kDa
EC 编号 ec_number	2.7.4.14
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	3791

MTAIAPVITIDGPSGAGKGTLCKAMAEALQWHLLDSGAIYRVLALAALHHHVDVASEDALVPLASHLDVRFVSTNGNLEVILEGEDVSGEIRTQEVANAASQVAAFPRVREALLRRQRAFRELPGLIADGRDMGTVVFPDAPVKIFLDASSEERAHRRMLQLQEKGFSVNFERLLAEIKERDDRDRNRAVAPLVPAADALVLDSTTLSIEQVIEKALQYARQKLALA

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	307.2 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	345

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kdpa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

Domain ID domain_id	d1kdpb_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.1 — Nucleotide and nucleoside kinases

CATH v4.4 (2 domains)

Domain ID domain_id	1kdpA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

Domain ID domain_id	1kdpB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	300 — P-loop containing nucleotide triphosphate hydrolases

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8. Citations (1)

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Unit-cell length a length_a	73.779 Å
Unit-cell length b length_b	75.981 Å
Unit-cell length c length_c	78.086 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2190
R_free r_free	0.2550

fit	/app/data/saxs_computation/kd/1kdp/1kdp.fit
pddf	/app/data/pr_computation/kd/1kdp/1kdp.pr.out
profile	/app/data/saxs_computation/kd/1kdp/1kdp.dat

CYTIDINE MONOPHOSPHATE KINASE FROM E. COLI IN COMPLEX WITH 2'-DEOXY-CYTIDINE MONOPHOSPHATE

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

CYTIDYLATE KINASE

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