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4k33

Crystal Structure of FGF Receptor 3 (FGFR3) Kinase Domain Harboring the K650E Mutation, a Gain-of-Function Mutation Responsible for Thanatophoric Dysplasia Type II and Spermatocytic Seminoma

Method: X-RAY DIFFRACTION Dmax: 68.3 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Fibroblast growth factor receptor 3

Homo sapiens

UniProt P22607

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 449–759 Fragment：Human FGF Receptor 3 Kinase Domain Mutation：C482A, C582S, K650E ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；100mM HEPES pH7.5, 19% PEG 4000, 4% C4H10O2, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.34 Å R-free 0.228

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 4K33 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1RY7 Crystal Structure of the 3 Ig form of FGFR3c in complex with FGF1 Deposited 2003-12-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 33–365（333 aa） Fragment：FGFR-3c
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Peg 4000, glycerol, MPD, cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.20 Å R-free 0.341
2LZL FGFR3tm Deposited 2012-10-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 357–399（43 aa） Fragment：UNP residues 357-399
Chain B 357–399（43 aa） Fragment：UNP residues 357-399
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.7；313 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition 0.75 mM [U-99% 13C; U-99% 15N] FGFR3tm, 0.75 mM FGFR3tm, 88 mM [U-99% 2H] DPC, 10 mM [U-99% 2H] SDS, 0.3 mM sodium azide, 6 mM TCEP, 5 mM citric acid, 15 mM Na2HPO4, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6LVM Crystal structure of FGFR3 in complex with pyrimidine derivative Deposited 2020-02-04 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 472–759（288 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EVR 2-[[5-[2-(3,5-dimethoxyphenyl)ethyl]-2-[[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]pyrimidin-4-yl]amino]-N-ethyl-benzenesulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；296 K；Citric Acid, PEG 8000
Resolution 2.53 Å R-free 0.279
6PNX Crystal Structure of an Asymmetric Dimer of FGF Receptor 3 Kinases Trapped in A-loop Tyrosine Transphosphorylation Reaction Deposited 2019-07-03 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 451–759（309 aa）
Chain B 451–759（309 aa）
Mutation：C482A, C582S, R669E Mutation：C482A, C582S, R669E ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；0.1 M Hepes, pH 7.5, and 1.8 M (NH4)2SO4
Resolution 2.20 Å R-free 0.230
7DHL Crystal structure of FGFR3 in complex with pyrimidine derivative Deposited 2020-11-16 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 472–759（288 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) H6X 5-[2-(3,5-dimethoxyphenyl)ethyl]-N-[3-methoxy-4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]pyrimidin-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；Citric Acid, Ammonium dihydrogen phosphate, PEG 3350
Resolution 2.57 Å R-free 0.254
7YSU Cryo-EM Structure of FGF23-FGFR3c-aKlotho-HS Quaternary Complex Deposited 2022-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 148–358（211 aa）
Chain E 148–358（211 aa）
Not recorded ZN ZINC ION × 1 CU COPPER (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8UDT The X-RAY co-crystal structure of human FGFR3 and KIN-3248 Deposited 2023-09-29 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 455–756（302 aa） Fragment：kinase domain
Mutation：residues 572-585 replaced by Ser-Gly MLT D-MALATE × 2 WGF 3-[(1-cyclopropyl-4,6-difluoro-1H-benzimidazol-5-yl)ethynyl]-1-[(3R,5R)-5-(methoxymethyl)-1-propanoylpyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.20 M DL-Malic acid pH 5.00, 18.00 % (w/v) PEG 4000
Resolution 2.83 Å R-free 0.274
8UDT The X-RAY co-crystal structure of human FGFR3 and KIN-3248 Deposited 2023-09-29 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 455–756（302 aa） Fragment：kinase domain
Mutation：residues 572-585 replaced by Ser-Gly WGF 3-[(1-cyclopropyl-4,6-difluoro-1H-benzimidazol-5-yl)ethynyl]-1-[(3R,5R)-5-(methoxymethyl)-1-propanoylpyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.20 M DL-Malic acid pH 5.00, 18.00 % (w/v) PEG 4000
Resolution 2.83 Å R-free 0.274
8UDT The X-RAY co-crystal structure of human FGFR3 and KIN-3248 Deposited 2023-09-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 455–756（302 aa） Fragment：kinase domain
Mutation：residues 572-585 replaced by Ser-Gly WGF 3-[(1-cyclopropyl-4,6-difluoro-1H-benzimidazol-5-yl)ethynyl]-1-[(3R,5R)-5-(methoxymethyl)-1-propanoylpyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.20 M DL-Malic acid pH 5.00, 18.00 % (w/v) PEG 4000
Resolution 2.83 Å R-free 0.274
8UDU The X-RAY co-crystal structure of human FGFR3 and Compound 17 Deposited 2023-09-29 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 455–756（302 aa） Fragment：kinase domain
Mutation：residues 572-585 replaced by Ser-Gly CL CHLORIDE ION × 1 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M Magnesium Chloride, 0.10 M TRIS/HCl pH 8.10, 0.20 M Sodium Chloride, 20.00 % (w/v) PEG 3350
Resolution 1.74 Å R-free 0.256
8UDU The X-RAY co-crystal structure of human FGFR3 and Compound 17 Deposited 2023-09-29 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 455–756（302 aa） Fragment：kinase domain
Mutation：residues 572-585 replaced by Ser-Gly CL CHLORIDE ION × 1 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M Magnesium Chloride, 0.10 M TRIS/HCl pH 8.10, 0.20 M Sodium Chloride, 20.00 % (w/v) PEG 3350
Resolution 1.74 Å R-free 0.256
8UDV The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 Deposited 2023-09-29 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 455–756（302 aa） Fragment：kinase domain
Mutation：V555M and residues 572-585 (Uniprot numbering) replaced by Ser-Gly SO4 SULFATE ION × 3 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M BIS-TRIS/HCl pH 6.50, 0.20 M (NH4)2SO4, 25.00 % (w/v) PEG 3350
Resolution 2.35 Å R-free 0.261
8UDV The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 Deposited 2023-09-29 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 455–756（302 aa） Fragment：kinase domain
Mutation：V555M and residues 572-585 (Uniprot numbering) replaced by Ser-Gly SO4 SULFATE ION × 2 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M BIS-TRIS/HCl pH 6.50, 0.20 M (NH4)2SO4, 25.00 % (w/v) PEG 3350
Resolution 2.35 Å R-free 0.261
8UDV The X-RAY co-crystal structure of human FGFR3 V555M and Compound 17 Deposited 2023-09-29 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 455–756（302 aa） Fragment：kinase domain
Mutation：V555M and residues 572-585 (Uniprot numbering) replaced by Ser-Gly SO4 SULFATE ION × 2 WIQ 3-[(6-chloro-1-cyclopropyl-1H-benzimidazol-5-yl)ethynyl]-1-[(3S,5S)-5-(methoxymethyl)-1-(prop-2-enoyl)pyrrolidin-3-yl]-5-(methylamino)-1H-pyrazole-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.10 M BIS-TRIS/HCl pH 6.50, 0.20 M (NH4)2SO4, 25.00 % (w/v) PEG 3350
Resolution 2.35 Å R-free 0.261
9CD7 FGFR3 Kinase Domain with Inhibitor TYRA-300 Deposited 2024-06-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 448–759（312 aa）
Mutation：C482A, C582S, K650E A1AV2 (3P)-5-[(1R)-1-(3,5-dichloropyridin-4-yl)ethoxy]-3-{6-[6-(methanesulfonyl)-2,6-diazaspiro[3.3]heptan-2-yl]pyridin-3-yl}-1H-indazole × 1 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate
Resolution 2.53 Å R-free 0.267
9CD7 FGFR3 Kinase Domain with Inhibitor TYRA-300 Deposited 2024-06-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 448–759（312 aa）
Mutation：C482A, C582S, K650E A1AV2 (3P)-5-[(1R)-1-(3,5-dichloropyridin-4-yl)ethoxy]-3-{6-[6-(methanesulfonyl)-2,6-diazaspiro[3.3]heptan-2-yl]pyridin-3-yl}-1H-indazole × 1 GOL GLYCEROL × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate
Resolution 2.53 Å R-free 0.267
9CD7 FGFR3 Kinase Domain with Inhibitor TYRA-300 Deposited 2024-06-24 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 448–759（312 aa）
Mutation：C482A, C582S, K650E A1AV2 (3P)-5-[(1R)-1-(3,5-dichloropyridin-4-yl)ethoxy]-3-{6-[6-(methanesulfonyl)-2,6-diazaspiro[3.3]heptan-2-yl]pyridin-3-yl}-1H-indazole × 1 GOL GLYCEROL × 6 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.25；291 K；17% PEG Smear Medium 10% Tacsimate pH 5.25 0.2M Ammonium Sulfate
Resolution 2.53 Å R-free 0.267
9D1X Crystal structure of FGFR3 bound to indazole inhibitor Deposited 2024-08-08 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 455–756（302 aa） Fragment：kinase domain
Mutation：P572S, P573G A1A6M (3P)-N-(2,6-dimethylphenyl)-6-methoxy-3-(1-methyl-1H-pyrazol-4-yl)-1H-indazole-5-carboxamide × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.1；293 K；0.2 M magnesium chloride, 0.3 M sodium chloride, 23% (w/v) PEG 3350, 0.1 M Tris-HCl pH 8.1
Resolution 1.60 Å R-free 0.190
9EKO A chimeric hybrid protein fused with the FGFR3 Transmembrane Domain Deposited 2024-12-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 371–399（29 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.287
9KFU Human FGFR3 in complex with inhibitor F1 Deposited 2024-11-07 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 448–756（309 aa）
Not recorded A1L5T (7~{S})-2-azanyl-7-(4-fluorophenyl)-6,7-dihydro-4~{H}-[1,3]thiazolo[4,5-b]pyridin-5-one × 1 SO4 SULFATE ION × 4 CO COBALT (II) ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293.15 K；25mM HEPES pH7.5, 1.8-2.0 M LiSO4, 10 Mm CoCl2
Resolution 1.40 Å R-free 0.251
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27 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 455–756（302 aa）
Not recorded A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 2.65 Å R-free 0.312
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27 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 455–756（302 aa）
Not recorded A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 2.65 Å R-free 0.312
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 455–756（302 aa）
Not recorded A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 2.65 Å R-free 0.312
9VM9 Crystal structure of FGFR3 in complex with 10s Deposited 2025-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 455–756（302 aa）
Not recorded A1ESW ~{N}-[1-methyl-3-[2-[[5-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 2.65 Å R-free 0.312
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27 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 455–756（302 aa）
Not recorded A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 1.97 Å R-free 0.237
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27 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 455–756（302 aa）
Not recorded A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 1.97 Å R-free 0.237
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 455–756（302 aa）
Not recorded A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 1.97 Å R-free 0.237
9VMB The X-RAY co-crystal structure of human FGFR3 and Compound 10t Deposited 2025-06-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 455–756（302 aa）
Not recorded A1ESX ~{N}-[1-methyl-3-[2-[[3-methyl-1-(2-morpholin-4-ylethyl)pyrazol-4-yl]amino]pyrimidin-4-yl]indol-6-yl]propanamide × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；25% (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES, pH 7.5
Resolution 1.97 Å R-free 0.237

15 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGFR3_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 15–325； UniProt 449–759

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 4k33

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4k33
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4k33
Deposition date deposition_date2013-04-10
Structure title titleCrystal Structure of FGF Receptor 3 (FGFR3) Kinase Domain Harboring the K650E Mutation, a Gain-of-Function Mutation Responsible for Thanatophoric Dysplasia Type II and Spermatocytic Seminoma
Keywords keywordsKinase Domain Fold Consisting of N- and C-lobes, Receptor Tyrosine Kinase, TRANSFERASE; 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_guinier20.60 Å
Radius of gyration Rg (electron density) rg_electron19.66 Å
Forward intensity I(0) i019763300.00
Molecular weight molecular_weight33543.0 kDa
Excluded volume excluded_volume41954 ų
Envelope volume envelope_volume50283 ų
Hydration-shell volume shell_volume21142 ų
Envelope diameter envelope_diameter67.1 Å
Shell Rg shell_rg26.44 Å
Envelope Rg envelope_rg20.17 Å
Shape Rg shape_rg19.68 Å
Total Rg total_rg20.53 Å
Total atoms total_atoms2349
Residues n_residues293
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 dmax68.3 Å
Rg (real space) rg_real20.53 Å
Rg uncertainty (real space) rg_real_error0.52 Å
I(0) (real space) i0_real1.9760e+07
I(0) uncertainty (real space) i0_real_error2.5890e+05
Rg (reciprocal space) rg_reciprocal20.54 Å
I(0) (reciprocal space) i0_reciprocal19760000.0000
Solution quality estimate total_estimate0.8049
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary24.8 Å
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.372
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5485000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.821; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000
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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd4k33a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id4k33A01
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_id4k33A02
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)