SAXSdb — 3mtl

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

Cell division protein kinase 16

Homo sapiens

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 163–478	Fragment：residues in UNP 163-478 Mutation：S319D	FEF (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME} × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；2.1M Na-formate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.40 Å R-free 0.263
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 163–478	Fragment：residues in UNP 163-478 Mutation：S319D	FEF (2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME} × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7；293 K；2.1M Na-formate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, temperature 293K	Resolution 2.40 Å R-free 0.263

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 3MTL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5G6V Crystal structure of the PCTAIRE1 kinase in complex with inhibitor Deposited 2016-08-16	Different construct 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 163–478（316 aa） Fragment：KINASE DOMAIN, RESIDUES 163-478	Mutation：YES	919 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；25% PEG MEDIUM SMEAR (PEG 2000, PEG 3350, PEG 4000, PEG 5000MME) AND 0.1 M CITRATE PH 5.5	Resolution 2.20 Å R-free 0.271
5G6V Crystal structure of the PCTAIRE1 kinase in complex with inhibitor Deposited 2016-08-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 163–478（316 aa） Fragment：KINASE DOMAIN, RESIDUES 163-478	Mutation：YES	919 4-[4-({[3-tert-butyl-1-(quinolin-6-yl)-1H-pyrazol-5-yl]carbamoyl}amino)-3-fluorophenoxy]-N-methylpyridine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；25% PEG MEDIUM SMEAR (PEG 2000, PEG 3350, PEG 4000, PEG 5000MME) AND 0.1 M CITRATE PH 5.5	Resolution 2.20 Å R-free 0.271
9R2I Cryo-EM structure of the complex CDK16:CCNY:14-3-3 Deposited 2025-04-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 107–496（390 aa）	Not recorded	MG MAGNESIUM ION × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8；20 mM HEPES buffer (pH 8.0), 150 mM NaCl, 4 mM MgCl2, 0.5 mM TCEP and 7.8 mM CHAPSO and supplemented with 2 mM ATP-gamma-S cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CDK16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–317； UniProt 163–478

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	3mtl
Deposition date deposition_date	2010-04-30
Structure title title	Crystal structure of the PCTAIRE1 kinase in complex with Indirubin E804
Keywords keywords	PCTAIRE1, kinase, Indirubin, Structural Genomics, Structural Genomics Consortium, SGC, 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	21.16 Å
Radius of gyration Rg (electron density) rg_electron	20.05 Å
Forward intensity I(0) i0	17249900.00
Molecular weight molecular_weight	32573.0 kDa
Excluded volume excluded_volume	41227 Å³
Envelope volume envelope_volume	49008 Å³
Hydration-shell volume shell_volume	20672 Å³
Envelope diameter envelope_diameter	73.0 Å
Shell Rg shell_rg	26.53 Å
Envelope Rg envelope_rg	20.46 Å
Shape Rg shape_rg	20.05 Å
Total Rg total_rg	20.97 Å
Total atoms total_atoms	2304
Residues n_residues	294
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	74.6 Å
Rg (real space) rg_real	21.12 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.7250e+07
I(0) uncertainty (real space) i0_real_error	2.5120e+05
Rg (reciprocal space) rg_reciprocal	21.13 Å
I(0) (reciprocal space) i0_reciprocal	17250000.0000
Solution quality estimate total_estimate	0.6342
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.322
Kurtosis Kurtosis kurtosis	-0.274
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5218000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.725; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.962; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cell division protein kinase 16
Molecular weight formula_weight	37308.8 kDa
EC 编号 ec_number	2.7.11.22
Mutation mutation	S319D
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	2414

METYIKLDKLGEGTYATVYKGKSKLTDNLVALKEIRLEHEEGAPCTAIREVSLLKDLKHANIVTLHDIIHTEKSLTLVFEYLDKDLKQYLDDCGNIINMHNVKLFLFQLLRGLAYCHRQKVLHRDLKPQNLLINERGELKLADFGLARAKSIPTKTYDNEVVTLWYRPPDILLGSTDYSTQIDMWGVGCIFYEMATGRPLFPGSTVEEQLHFIFRILGTPTEETWPGILSNEEFKTYNYPKYRAEALLSHAPRLDSDGADLLTKLLQFEGRNRISAEDAMKHPFFLSLGERIHKLPDTTSIFALKEIQLQKEASLRSAHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	;(2Z,3E)-2,3'-BIINDOLE-2',3(1H,1'H)-DIONE 3-{O-[(3R)-3,4-DIHYDROXYBUTYL]OXIME} ;
Molecular weight formula_weight	365.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	101

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3mtlA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	3mtlA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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8. Citations (1)

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Unit-cell length a length_a	47.390 Å
Unit-cell length b length_b	47.390 Å
Unit-cell length c length_c	341.310 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 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	20.090 Å
R factor r_factor	0.1979
R_work r_work	0.1938
R_free r_free	0.2633

fit	/app/data/saxs_computation/mt/3mtl/3mtl.fit
pddf	/app/data/pr_computation/mt/3mtl/3mtl.pr.out
profile	/app/data/saxs_computation/mt/3mtl/3mtl.dat

Crystal structure of the PCTAIRE1 kinase in complex with Indirubin E804

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

Cell division protein kinase 16

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