4dum

Co-crystal structure of eIF4E with inhibitor

Method: X-RAY DIFFRACTION D_max: 73.2 Å Quality: GOOD

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

Eukaryotic translation initiation factor 4E

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 1–217	Not recorded	HLI (4-{7-[2-(4-chlorophenoxy)ethyl]-2-(methylamino)-6-oxo-6,7-dihydro-1H-purin-8-yl}phenyl)phosphonic acid × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；289 K；The purified protein which contained 100 uM m7-GTP was then concentrated to about 7 mg/mL in 20 mM Hepes, pH7.6, 100 mM KCl, 1mM DTT, 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.95 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 4DUM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1IPB CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GPPPA Deposited 2001-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa）	Not recorded	GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.229
1IPC CRYSTAL STRUCTURE OF EUKARYOTIC INITIATION FACTOR 4E COMPLEXED WITH 7-METHYL GTP Deposited 2001-05-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa）	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.228
1WKW Crystal structure of the ternary complex of eIF4E-m7GpppA-4EBP1 peptide Deposited 2004-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–217（191 aa） Fragment：RESIDUES 27-217	Not recorded	GTA P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG 4000, isopropanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.270
2GPQ Cap-free structure of eIF4E suggests basis for its allosteric regulation Deposited 2006-04-18	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；293 K；Ionic strength (raw mmCIF value) 100 mM NaCl；Pressure ambient NMR sample composition 0.3mM eIF4E U-98% 15N, U-13C; 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O NMR sample composition 0.3mM eIF4E U-98% 15N, U-95% D; 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 50mM phosphate buffer; 100mM NaCl; 1mM DTT; 0.02% NaN3; 90% H2O, 10% D2O	Resolution not provided
2V8W Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 2.30 Å R-free 0.243
2V8W Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 2.30 Å R-free 0.243
2V8X Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGQ 7-BENZYL GUANINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0	Resolution 2.30 Å R-free 0.259
2V8X Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–217（217 aa）	Not recorded	MGQ 7-BENZYL GUANINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0	Resolution 2.30 Å R-free 0.259
2V8Y Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGV P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0	Resolution 2.10 Å R-free 0.250
2V8Y Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives Deposited 2007-08-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 1–217（217 aa）	Not recorded	MGV P-FLUORO-7-BENZYL GUANINE MONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；25% PEG 6000, 7% AMMONIUM SULPHATE, 100MM HEPES-KOH PH 7.0	Resolution 2.10 Å R-free 0.250
2W97 Crystal Structure of eIF4E Bound to Glycerol and eIF4G1 peptide Deposited 2009-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–217（217 aa） Chain B 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 PGE TRIETHYLENE GLYCOL × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；60% AMMONIUM SULPHATE, 100MM TRIS-HCL PH 8.0, 1% PEG400	Resolution 2.29 Å R-free 0.239
3AM7 Crystal structure of the ternary complex of eIF4E-M7GTP-4EBP2 peptide Deposited 2010-08-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–217（191 aa） Fragment：UNP RESIDUES 27-217	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；20% PEG-MME 2000, 0.1M MES, 0.2M ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K	Resolution 2.20 Å R-free 0.268
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa）	Not recorded	UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K	Resolution 2.10 Å R-free 0.260
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–217（217 aa）	Not recorded	UNX UNKNOWN LIGAND × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K	Resolution 2.10 Å R-free 0.260
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–217（217 aa）	Not recorded	UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K	Resolution 2.10 Å R-free 0.260
3TF2 Crystal structure of the cap free human translation initiation factor eIF4E Deposited 2011-08-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–217（217 aa）	Not recorded	UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；289 K；20% PEG-3350, 0.2 M diammonium citrate, vapor diffusion, temperature 289K	Resolution 2.10 Å R-free 0.260
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	SO4 SULFATE ION × 1 UNX UNKNOWN LIGAND × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K	Resolution 2.10 Å R-free 0.224
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–217（217 aa）	Not recorded	SO4 SULFATE ION × 3 UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K	Resolution 2.10 Å R-free 0.224
3U7X Crystal structure of the human eIF4E-4EBP1 peptide complex without cap Deposited 2011-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–217（217 aa） Chain B 1–217（217 aa）	Not recorded	SO4 SULFATE ION × 4 UNX UNKNOWN LIGAND × 20	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；1:1 of (protein stock: 0.0004 M eif4e, 0.001 M 4epb1, 0.004 M ribavirin, 0.02 HEPES, 0.1 M potassium chloride, 0.001 tcep, ph 7.3):(reservoir: 2 M ammonium sulfate, 2% Peg-400, 0.1 M sodium HEPES), vapor diffusion, sitting drop, temperature 291K	Resolution 2.10 Å R-free 0.224
4AZA Improved eIF4E binding peptides by phage display guided design. Deposited 2012-06-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；20% PEG 5000 MME, 100 MM BISTRIS PH 6.5.	Resolution 2.16 Å R-free 0.279
4AZA Improved eIF4E binding peptides by phage display guided design. Deposited 2012-06-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；20% PEG 5000 MME, 100 MM BISTRIS PH 6.5.	Resolution 2.16 Å R-free 0.279
4BEA Crystal Structure of eIF4E in Complex with a Stapled Peptide Derivative Deposited 2013-03-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；18-26% OF POLYETHYLENE GLYCOL 3350, 0.01-02M AMMONIUM SULPHATE AND 100MM BIS-TRIS AT PH 5.5	Resolution 2.57 Å R-free 0.266
4DT6 Co-crystal structure of eIF4E with inhibitor Deposited 2012-02-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–217（217 aa）	Not recorded	6LI 7-[2-(4-chlorophenoxy)ethyl]guanosine 5'-(dihydrogen phosphate) × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；The purified protein which contained 100 uM m7-GTP was concentrated to about 7 mg/mL in 20 mM Hepes, pH 7.6, 100 mM KCl, 1mM DTT, and 0.1 mM EDTA for crystallization. The m7-GTP-bound eIF4e protein was crystallized with 1:1 ratio of protein solution to reservoir solution of 17-20% PEG-3350 and 0.1-0.4M Na formate, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.60 Å R-free 0.267
4TPW The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 33R (2E)-2-{2-[(4P)-4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN	Resolution 1.50 Å R-free 0.193
4TPW The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN	Resolution 1.50 Å R-free 0.193
4TQB The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 34K (2E)-2-{2-[4-(4-bromophenyl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 12-20%, 100mM MES pH 6.5, 10% IPN	Resolution 1.59 Å R-free 0.211
4TQB The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 12-20%, 100mM MES pH 6.5, 10% IPN	Resolution 1.59 Å R-free 0.211
4TQC The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1 34J (2S)-3-(4-amino-3-nitrophenyl)-2-{2-[(4P)-4-(3,4-dichlorophenyl)-1,3-thiazol-2-yl]hydrazin-1-yl}propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG 4000 12-20%, 100mM MES pH 8.5, 10% IPN	Resolution 1.80 Å R-free 0.194
4TQC The co-complex structure of the translation initiation factor eIF4E with the inhibitor 4EGI-1 reveals an allosteric mechanism for dissociating eIF4G Deposited 2014-06-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；290 K；PEG 4000 12-20%, 100mM MES pH 8.5, 10% IPN	Resolution 1.80 Å R-free 0.194
4UED Complex of human eIF4E with the 4E binding protein 4E-BP1 Deposited 2014-12-16	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 36–217（182 aa） Fragment：RESIDUES 36-217	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；0.03M EACH DIETHYLENE GLYCOL, TRIETHYLENE GLYCOL, TETRAETHYLENE GLYCOL, PENTAETHYLENE GLYCOL, 0.1M BICINE/TRIZMA BASE PH 8.5, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD	Resolution 1.75 Å R-free 0.237
5EHC Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-10-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	5NX 3-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-chlorophenyl)methyl]-6-oxidanylidene-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding	Resolution 2.40 Å R-free 0.264
5EI3 Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-10-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	5O8 ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-1,1,1-tris(fluoranyl)methanesulfonamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding	Resolution 1.71 Å R-free 0.187
5EIR Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-10-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	5O8 ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-6-oxidanylidene-7-(phenylmethyl)-1~{H}-purin-7-ium-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-1,1,1-tris(fluoranyl)methanesulfonamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1???3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding. Crystals replaced in to above conditions without (NH4)2SO4 prior to freezing.	Resolution 2.69 Å R-free 0.272
5EKV Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-11-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	5PQ 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1-3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding	Resolution 3.61 Å R-free 0.342
5EKV Co-crystal structure of eIF4E with nucleotide mimetic inhibitor. Deposited 2015-11-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–217（217 aa）	Not recorded	5PQ 3-[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-4-oxidanyl-cyclobut-3-ene-1,2-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；21-31% PEG 8000, 1-3% (NH4)2SO4, 100 mM HEPES, pH 7.5, 1 round of seeding	Resolution 3.61 Å R-free 0.342
5GW6 Water-Bridge Mediates Recognition of mRNA Cap in eIF4E Deposited 2016-09-08	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 23–217（195 aa）	Mutation：E105A, K106A, K108A	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；20% PEG 5000 MME, 100MM TRIS BIS PH 5.0, 0.05M AMMONIUM SULPHATE	Resolution 1.97 Å R-free 0.228
5T46 Crystal structure of the human eIF4E-eIF4G complex Deposited 2016-08-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；0.1 M Hepes pH 7.25, 25% w/v PEG 6000	Resolution 1.53 Å R-free 0.162
5T46 Crystal structure of the human eIF4E-eIF4G complex Deposited 2016-08-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–217（217 aa）	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.25；293 K；0.1 M Hepes pH 7.25, 25% w/v PEG 6000	Resolution 1.53 Å R-free 0.162
5ZJY Stapled-peptides tailored against initiation of translation Deposited 2018-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；30%(W/V) PEG 6000, 0.1M Na-Hepes pH6.5	Resolution 1.59 Å R-free 0.216
5ZJZ Stapled-peptides tailored against initiation of translation Deposited 2018-03-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；12.5%(w/v) PEG20000, 20%(w/v) PEG MME 550, 0.1M MES/imidazole pH 6.5	Resolution 1.67 Å R-free 0.212
5ZK5 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–217（190 aa）	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；30%(w/v) PEG6000, 0.1M Na-Hepes pH 6.5	Resolution 2.25 Å R-free 0.268
5ZK7 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 IOD IODIDE ION × 4 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2M Potassium Iodide, 0.1M MES/Imidazole pH6.5, 25%(wv) PEG4000	Resolution 2.12 Å R-free 0.270
5ZK7 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 28–217（190 aa） Fragment：UNP residues 28-217	Not recorded	MGT 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE × 1 IOD IODIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；0.2M Potassium Iodide, 0.1M MES/Imidazole pH6.5, 25%(wv) PEG4000	Resolution 2.12 Å R-free 0.270
5ZK9 Stapled-peptides tailored against initiation of translation Deposited 2018-03-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 28–217（190 aa）	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；12.5% pEG1000 w/v, 12.5% PEG3350 w/v, 12.5% MPD w/v, 0.1M MES/imidazole pH 6.5	Resolution 1.76 Å R-free 0.211
5ZML Stapled-peptides tailored against initiation of translation Deposited 2018-04-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 27–217（191 aa）	Not recorded	NO3 NITRATE ION × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；40%(v/v) Ethylene glycol, 20 %(w/v) PEG 8000, 0.3M Sodium nitrate, 0.3M Ammonium sulfate, 100mM Sodium HEPES/MOPS pH 7.5	Resolution 1.80 Å R-free 0.223
7D6Y eIF4E in Complex with a Disulphide-Free Autonomous VH Domain Deposited 2020-10-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；25% (w/v) PEG 6000, 0.01-02 M Ammonium Sulphate, 100mM Tris, pH 8.5	Resolution 1.67 Å R-free 0.206
7D8B Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways Deposited 2020-10-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.01M Tri-sodium citrate, 16% PEG 6000	Resolution 2.46 Å R-free 0.292
7D8B Engineering Disulphide-Free Autonomous Antibody VH Domains to modulate intracellular pathways Deposited 2020-10-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–217（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.01M Tri-sodium citrate, 16% PEG 6000	Resolution 2.46 Å R-free 0.292
7EZW Cyclic Peptide that Interacts with the eIF4E Capped-mRNA Binding Site Deposited 2021-06-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Potassium chloride 20% (w/v) PEG 3350	Resolution 2.35 Å R-free 0.248
7F07 Autonomous VH domain that interacts with eIF4E at the Capped mRNA Binding site. Deposited 2021-06-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M TRIS.HCl pH 8.5 25% (v/v) PEG 550 MME	Resolution 2.25 Å R-free 0.266
7MEU A biphenyl inhibitor of eIF4E targeting an internal binding site enables the design of cell-permeable PROTAC-degraders Deposited 2021-04-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–217（191 aa）	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1 Z5D (2E)-2-{2-[4-([1,1'-biphenyl]-4-yl)-1,3-thiazol-2-yl]hydrazinylidene}-3-(2-nitrophenyl)propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN	Resolution 1.91 Å R-free 0.219
7MEU A biphenyl inhibitor of eIF4E targeting an internal binding site enables the design of cell-permeable PROTAC-degraders Deposited 2021-04-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 27–217（191 aa）	Not recorded	MGP 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；PEG 4000 10-20%, 100mM MES pH 6.5, 10% IPN	Resolution 1.91 Å R-free 0.219
7XTP eIF4E in Complex with a Disulphide-Free Autonomous VH Domain Deposited 2022-05-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium HEPES pH7.5, 25% PEG 6000	Resolution 1.83 Å R-free 0.259
7XTP eIF4E in Complex with a Disulphide-Free Autonomous VH Domain Deposited 2022-05-17	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–217（217 aa）	Not recorded	MGO [[(2R,3S,4R,5R)-5-(6-AMINO-3-METHYL-4-OXO-5H-IMIDAZO[4,5-C]PYRIDIN-1-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHOXY-HYDROXY-PHOSPHORYL] PHOSPHONO HYDROGEN PHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium HEPES pH7.5, 25% PEG 6000	Resolution 1.83 Å R-free 0.259
8QM4 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21	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 36–217（182 aa） Chain B 36–217（182 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 2 PGE TRIETHYLENE GLYCOL × 2 W5B 3-phenylphenol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；273 K；0.002M DTT, 40% PEG 400, 0.1M pH=7.5 HEPES/NaOH	Resolution 1.85 Å R-free 0.217
8QM5 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21	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 36–217（182 aa） Chain B 36–217（182 aa）	Not recorded	W4U 1-(4-chlorophenyl)cyclopentane-1-carboxylic acid × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.002M DTT 40% PEG 400 0.1M pH=7.5 HEPES/NaOH	Resolution 1.89 Å R-free 0.220
8QM6 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21	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 36–217（182 aa） Chain B 36–217（182 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 3 W2N (1~{S})-1-[4-(2-fluorophenyl)phenyl]ethanol × 2 W4B (1~{R})-1-[4-(2-fluorophenyl)phenyl]ethanol × 2 PEG DI(HYDROXYETHYL)ETHER × 1 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.002M DTT 40% PEG 400 0.1M pH=8 Tris/HCl	Resolution 1.93 Å R-free 0.227
8QM7 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21	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 36–217（182 aa） Chain B 36–217（182 aa）	Not recorded	DMS DIMETHYL SULFOXIDE × 3 PGE TRIETHYLENE GLYCOL × 1 W5K (2~{R})-2-[(1~{R})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol × 2 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.002M DTT 38% PEG 400 0.1M pH=8 Tris/HCl	Resolution 2.19 Å R-free 0.240
8QM8 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21	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 36–217（182 aa） Chain B 36–217（182 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 6 PGE TRIETHYLENE GLYCOL × 1 W4K (2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol × 2 DMS DIMETHYL SULFOXIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；10% PEG 3350 0.1M pH=8 Bicine/NaOH	Resolution 1.58 Å R-free 0.202
8QM9 Potential drug binding sites for translation initiation factor eIF4E Deposited 2023-09-21	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 36–217（182 aa） Chain B 36–217（182 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 3 PEG DI(HYDROXYETHYL)ETHER × 4 DMS DIMETHYL SULFOXIDE × 2 W4K (2~{R})-2-[(1~{S})-1-[4-(2-fluorophenyl)-2-(2-hydroxyethylamino)phenyl]propoxy]propan-1-ol × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.002M DTT 38% PEG 400 0.1M pH=8 Tris/HCl	Resolution 1.97 Å R-free 0.272
8SX4 Crystal Structure of eIF4e in complex with Compound 7n Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–217（190 aa）	Not recorded	WXL [(~{Z})-4-[2-azanyl-7-[(5-chloranyl-1~{H}-indol-2-yl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]but-2-enyl]phosphonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16-26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2	Resolution 1.99 Å R-free 0.243
8SX4 Crystal Structure of eIF4e in complex with Compound 7n Deposited 2023-05-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–217（190 aa）	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；16-26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2	Resolution 1.99 Å R-free 0.243
9DON Crystal structure of eIF4e in complex with Compound 5-PA Deposited 2024-09-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 28–217（190 aa）	Not recorded	M7G 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2	Resolution 2.09 Å R-free 0.247
9DON Crystal structure of eIF4e in complex with Compound 5-PA Deposited 2024-09-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 28–217（190 aa）	Not recorded	A1A8P 2-[3-[[2-azanyl-7-[(5-chloranyl-1-benzofuran-2-yl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]methyl]phenyl]ethylphosphonic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；26% Peg 3350, 0.1 M MES pH 6.0, 10% isopropanol and 2 mM CaCl2	Resolution 2.09 Å R-free 0.247

44 other PDB entries and 64 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IF4E_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 24–240； UniProt 1–217

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4dum
Deposition date deposition_date	2012-02-22
Structure title title	Co-crystal structure of eIF4E with inhibitor
Keywords keywords	CAP-binding protein, translation initiation factor, m7GTP, TRANSLATION; TRANSLATION
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	18.24 Å
Radius of gyration Rg (electron density) rg_electron	17.10 Å
Forward intensity I(0) i0	9443070.00
Molecular weight molecular_weight	22494.0 kDa
Excluded volume excluded_volume	28088 Å³
Envelope volume envelope_volume	32958 Å³
Hydration-shell volume shell_volume	16452 Å³
Envelope diameter envelope_diameter	74.0 Å
Shell Rg shell_rg	23.10 Å
Envelope Rg envelope_rg	18.02 Å
Shape Rg shape_rg	17.06 Å
Total Rg total_rg	18.21 Å
Total atoms total_atoms	1587
Residues n_residues	187
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	73.2 Å
Rg (real space) rg_real	18.25 Å
Rg uncertainty (real space) rg_real_error	0.72 Å
I(0) (real space) i0_real	9.4430e+06
I(0) uncertainty (real space) i0_real_error	1.4490e+05
Rg (reciprocal space) rg_reciprocal	18.25 Å
I(0) (reciprocal space) i0_reciprocal	9443000.0000
Solution quality estimate total_estimate	0.7616
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.513
Kurtosis Kurtosis kurtosis	0.496
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2688000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.350; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.850; Smooth: 0.997

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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	Eukaryotic translation initiation factor 4E
Molecular weight formula_weight	28040.3 kDa
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	1613

MDYKDDDDKHHHHHHTENLYFQGMATVEPETTPTPNPPTTEEEKTESNQEVANPEHYIKHPLQNRWALWFFKNDKSKTWQANLRLISKFDTVEDFWALYNHIQLSSNLMPGCDYSLFKDGIEPMWEDEKNKRGGRWLITLNKQQRRSDLDRFWLETLLCLIGESFDDYSDDVCGAVVNVRAKGDKIAIWTTECENREAVTHIGRVYKERLGLPPKIVIGYQSHADTATKSGSTTKNRFVV

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	(4-{7-[2-(4-chlorophenoxy)ethyl]-2-(methylamino)-6-oxo-6,7-dihydro-1H-purin-8-yl}phenyl)phosphonic acid
Molecular weight formula_weight	475.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 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	14

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4duma_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.86 — eIF4e-like
Superfamily Superfamily superfamily	d.86.1 — eIF4e-like
Family Family family	d.86.1.1 — Translation initiation factor eIF4e

CATH v4.4 (1 domains)

Domain ID domain_id	4dumA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	760 — RNA Cap, Translation Initiation Factor Eif4e
Homologous superfamily homologous superfamily	10 — RNA Cap, Translation Initiation Factor Eif4e

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8. Citations (1)

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Unit-cell length a length_a	38.225 Å
Unit-cell length b length_b	58.766 Å
Unit-cell length c length_c	125.442 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	38.236 Å
R factor r_factor	0.2050
R_work r_work	0.2018
R_free r_free	0.2711

fit	/app/data/saxs_computation/du/4dum/4dum.fit
pddf	/app/data/pr_computation/du/4dum/4dum.pr.out
profile	/app/data/saxs_computation/du/4dum/4dum.dat