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5g6v

Crystal structure of the PCTAIRE1 kinase in complex with inhibitor

Method: X-RAY DIFFRACTION Dmax: 84.4 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

CYCLIN-DEPENDENT KINASE 16

HOMO SAPIENS

UniProt Q00536

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：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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 163–478 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

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 5G6V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3MTL Crystal structure of the PCTAIRE1 kinase in complex with Indirubin E804 Deposited 2010-04-30 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：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
3MTL Crystal structure of the PCTAIRE1 kinase in complex with Indirubin E804 Deposited 2010-04-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 163–478（316 aa） 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
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 Author chain B； 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.

SAXS scattering curve SAXS Profile

SAXS profile for 5g6v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5g6v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5g6v
Deposition date deposition_date2016-08-16
Structure title titleCrystal structure of the PCTAIRE1 kinase in complex with inhibitor
Keywords keywordsTRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier27.60 Å
Radius of gyration Rg (electron density) rg_electron26.58 Å
Forward intensity I(0) i074102900.00
Molecular weight molecular_weight69495.0 kDa
Excluded volume excluded_volume87891 ų
Envelope volume envelope_volume105730 ų
Hydration-shell volume shell_volume32773 ų
Envelope diameter envelope_diameter89.0 Å
Shell Rg shell_rg34.39 Å
Envelope Rg envelope_rg26.49 Å
Shape Rg shape_rg26.59 Å
Total Rg total_rg27.41 Å
Total atoms total_atoms4910
Residues n_residues610
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax84.4 Å
Rg (real space) rg_real27.51 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real7.4100e+07
I(0) uncertainty (real space) i0_real_error9.7380e+05
Rg (reciprocal space) rg_reciprocal27.54 Å
I(0) (reciprocal space) i0_reciprocal74100000.0000
Solution quality estimate total_estimate0.7201
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.1 Å
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.543
Angular range angular_range— – 0.2850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha24630000.0000
Real-space data points n_real_points58
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.962; Stabil: 1.000; Sysdev: 0.177; Positv: 1.000; Valcen: 1.000; Smooth: 0.941
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5g6vA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5g6vA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5g6vB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5g6vB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)