4ync

OYE1 W116A COMPLEXED WITH (Z)-METHYL-3-CYANO-3-PHENYLACRYLATE IN A NON PRODUCTIVE BINDING MODE

Method: X-RAY DIFFRACTION D_max: 66.3 Å Quality: GOOD

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

NADPH dehydrogenase 1

Saccharomyces pastorianus

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 2–398	Mutation：W116A	FMN FLAVIN MONONUCLEOTIDE × 1 4EG methyl (2Z)-3-cyano-3-phenylprop-2-enoate × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M NaHEPES, 35% PEG 400	Resolution 1.50 Å R-free 0.172

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 4YNC	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BWK OLD YELLOW ENZYME (OYE1) MUTANT H191N Deposited 1998-09-24	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 1–399（399 aa）	Mutation：H191N	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；pH 8.3	Resolution 2.30 Å R-free 0.254
1BWL OLD YELLOW ENZYME (OYE1) DOUBLE MUTANT H191N:N194H Deposited 1998-09-24	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 1–399（399 aa）	Mutation：H191N:N194H	FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.3；pH 8.3	Resolution 2.70 Å R-free 0.273
1K02 Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn Deposited 2001-09-18	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 1–399（399 aa）	Mutation：Q114N	MG MAGNESIUM ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；PEG-400, HEPES, Magnesium Chloride, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å
1K03 Crystal Structure of Old Yellow Enzyme Mutant Gln114Asn Complexed with Para-hydroxy Benzaldehyde Deposited 2001-09-18	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 1–399（399 aa）	Mutation：Q114N	MG MAGNESIUM ION × 1 FMN FLAVIN MONONUCLEOTIDE × 1 HBA P-HYDROXYBENZALDEHYDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；PEG-400, HEPES, Magnesium chloride, para-hydroxy benzaldehyde, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å
1OYA OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, LIGAND BINDING AND COMPARISON WITH RELATED FLAVOPROTEINS Deposited 1994-08-25	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 1–399（399 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.241
1OYB OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, LIGAND BINDING AND COMPARISON WITH RELATED FLAVOPROTEINS Deposited 1994-08-25	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 1–399（399 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2 HBA P-HYDROXYBENZALDEHYDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.236
1OYC OLD YELLOW ENZYME AT 2 ANGSTROMS RESOLUTION: OVERALL STRUCTURE, LIGAND BINDING AND COMPARISON WITH RELATED FLAVOPROTEINS Deposited 1994-08-25	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 1–399（399 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.259
3RND W116I-OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone Deposited 2011-04-22	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 2–400（399 aa）	Mutation：W116I	FMN FLAVIN MONONUCLEOTIDE × 2 3RN 2-(hydroxymethyl)cyclopent-2-en-1-one × 2 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.1M hepes, 35% PEG 400, 0.2M Mg2Cl2, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.40 Å R-free 0.168
3TX9 OYE1 complexed with 2-(Hydroxymethyl)-cyclopent-2-enone Deposited 2011-09-22	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 1–400（400 aa）	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 2 MG MAGNESIUM ION × 2 3RN 2-(hydroxymethyl)cyclopent-2-en-1-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M HEPES, 35-40% PEG400, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.00 Å R-free 0.216
3TXZ OYE1-W116Q complexed with R-carvone Deposited 2011-09-23	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 1–400（400 aa）	Mutation：W116Q	FMN FLAVIN MONONUCLEOTIDE × 1 07V (5R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.186
4GBU OYE1-W116A in complex with aromatic product of S-carvone dismutation Deposited 2012-07-28	Different construct 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 1–400（400 aa）	Mutation：W116A	MG MAGNESIUM ION × 4 0WV 2-methyl-5-(prop-1-en-2-yl)phenol × 2 CL CHLORIDE ION × 4 NA SODIUM ION × 10 1PE PENTAETHYLENE GLYCOL × 10 FMN FLAVIN MONONUCLEOTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；35% Peg400, 0.2M MgCl2, 0.1M Na Hepes, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.18 Å R-free 0.121
4GE8 OYE1-W116I complexed with (s)-Carvone Deposited 2012-08-01	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 1–400（400 aa）	Mutation：W116I	MG MAGNESIUM ION × 2 CL CHLORIDE ION × 6 NA SODIUM ION × 8 1PE PENTAETHYLENE GLYCOL × 8 FMN FLAVIN MONONUCLEOTIDE × 2 0WU (5S)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 35%peg400, 0.1M NaHepes, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.50 Å R-free 0.170
4GWE W116L-OYE1 complexed with (R)-carvone Deposited 2012-09-02	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 1–400（400 aa）	Mutation：W116L	FMN FLAVIN MONONUCLEOTIDE × 1 MG MAGNESIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 2 NA SODIUM ION × 2 CL CHLORIDE ION × 1 07V (5R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.1M hepes, 0.2M MgCl2, 35%peg400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.45 Å R-free 0.145
4GXM OYE1-W116L in complex with aromatic product of R-carvone dismutation Deposited 2012-09-04	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 1–400（400 aa）	Mutation：w116L	MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 1PE PENTAETHYLENE GLYCOL × 5 NA SODIUM ION × 4 FMN FLAVIN MONONUCLEOTIDE × 1 0WV 2-methyl-5-(prop-1-en-2-yl)phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M Hepes, 35%PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.36 Å R-free 0.137
4H4I OYE1-W116V complexed with the dismutation product of (S)-carvone Deposited 2012-09-17	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 1–400（400 aa）	Mutation：W116V	MG MAGNESIUM ION × 6 0WV 2-methyl-5-(prop-1-en-2-yl)phenol × 2 NA SODIUM ION × 10 1PE PENTAETHYLENE GLYCOL × 10 FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 35%PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.25 Å R-free 0.146
4H6K W116I mutant of OYE1 Deposited 2012-09-19	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 2–400（399 aa）	Mutation：W116I	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 2 1PE PENTAETHYLENE GLYCOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.1M hepes, 0.2M MgCl2, peg400 35%, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.204
4K7V OYE1-W116A complexed with (R)-carvone Deposited 2013-04-17	Different construct 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 1–400（400 aa）	Mutation：W116A	FMN FLAVIN MONONUCLEOTIDE × 2 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 07V (5R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one × 2 NA SODIUM ION × 4 1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.52 Å R-free 0.183
4K7Y Oye1-w116t Deposited 2013-04-17	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 1–400（400 aa）	Mutation：W116T	FMN FLAVIN MONONUCLEOTIDE × 2 MG MAGNESIUM ION × 6 PEG DI(HYDROXYETHYL)ETHER × 6 CL CHLORIDE ION × 4 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.20 Å R-free 0.135
4K8E OYE1-W116V complexed with the aromatic product of (R)-carvone dismutation Deposited 2013-04-18	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 1–400（400 aa）	Mutation：W116V	FMN FLAVIN MONONUCLEOTIDE × 2 MG MAGNESIUM ION × 4 CL CHLORIDE ION × 4 0WV 2-methyl-5-(prop-1-en-2-yl)phenol × 2 PEG DI(HYDROXYETHYL)ETHER × 2 NA SODIUM ION × 8 PGE TRIETHYLENE GLYCOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3 , VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.27 Å R-free 0.127
4K8H OYE1-W116V complexed with (R)-carvone Deposited 2013-04-18	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 1–400（400 aa）	Mutation：W116V	FMN FLAVIN MONONUCLEOTIDE × 2 CL CHLORIDE ION × 4 07V (5R)-2-methyl-5-(prop-1-en-2-yl)cyclohex-2-en-1-one × 2 NA SODIUM ION × 4 PGE TRIETHYLENE GLYCOL × 2 1PE PENTAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M HEPES, 30-40% PEG400, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.55 Å R-free 0.162
4RNU G303 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain A 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.68 Å R-free 0.283
4RNU G303 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain B 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.68 Å R-free 0.283
4RNU G303 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain C 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.68 Å R-free 0.283
4RNU G303 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain D 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.68 Å R-free 0.283
4RNV G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor p-Hydroxybenzaldehyde Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain A 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 HBA P-HYDROXYBENZALDEHYDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.47 Å R-free 0.249
4RNV G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor p-Hydroxybenzaldehyde Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain B 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 HBA P-HYDROXYBENZALDEHYDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.47 Å R-free 0.249
4RNV G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor p-Hydroxybenzaldehyde Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain C 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 HBA P-HYDROXYBENZALDEHYDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.47 Å R-free 0.249
4RNV G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor p-Hydroxybenzaldehyde Deposited 2014-10-26	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 303–397（95 aa） Fragment：UNP residues 303-397, 2-302 Chain D 2–302（301 aa） Fragment：UNP residues 303-397, 2-302	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 HBA P-HYDROXYBENZALDEHYDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；18% PEG 3350, 0.2 M MgCl2, 0.25% glucoside, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 2.47 Å R-free 0.249
4RNW Truncated version of the G303 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 307–397（91 aa） Fragment：UNP residues 307-397, 2-292 Chain A 2–292（291 aa） Fragment：UNP residues 307-397, 2-292	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20% PEG 10000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.55 Å R-free 0.231
4RNW Truncated version of the G303 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 307–397（91 aa） Fragment：UNP residues 307-397, 2-292 Chain B 2–292（291 aa） Fragment：UNP residues 307-397, 2-292	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；289 K；20% PEG 10000, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.55 Å R-free 0.231
4RNX K154 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 154–397（244 aa） Fragment：UNP residues 154-397, 2-153 Chain A 2–153（152 aa） Fragment：UNP residues 154-397, 2-153	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；30% PEG 2KMME, 0.1M Potassium Thiocyanate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.25 Å R-free 0.162
4RNX K154 Circular Permutation of Old Yellow Enzyme Deposited 2014-10-26	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 154–397（244 aa） Fragment：UNP residues 154-397, 2-153 Chain B 2–153（152 aa） Fragment：UNP residues 154-397, 2-153	Not recorded	FMN FLAVIN MONONUCLEOTIDE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；289 K；30% PEG 2KMME, 0.1M Potassium Thiocyanate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 1.25 Å R-free 0.162
4YIL OYE1 W116A COMPLEXED WITH (Z)-METHYL 3-CYANO-3-(4-FLUOROPHENYL)ACRYLATE IN A NON PRODUCTIVE BINDING MODE Deposited 2015-03-02	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–398（397 aa）	Mutation：W116A	FMN FLAVIN MONONUCLEOTIDE × 1 MG MAGNESIUM ION × 1 NA SODIUM ION × 1 4D3 methyl (2Z)-3-cyano-3-(4-fluorophenyl)prop-2-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；0.2M MgCl2, 0.1M Na HEPES, 35% PEG 400,	Resolution 1.46 Å R-free 0.189

25 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	OYE1_SACPS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–397； UniProt 2–398

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	4ync
Deposition date deposition_date	2015-03-09
Structure title title	OYE1 W116A COMPLEXED WITH (Z)-METHYL-3-CYANO-3-PHENYLACRYLATE IN A NON PRODUCTIVE BINDING MODE
Keywords keywords	OXIDOREDUCTASE, CATALYTIC ACTIVITY, FMN BINDING, OLD YELLOW ENZYME; OXIDOREDUCTASE
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	21.22 Å
Radius of gyration Rg (electron density) rg_electron	20.02 Å
Forward intensity I(0) i0	34158200.00
Molecular weight molecular_weight	45183.0 kDa
Excluded volume excluded_volume	56449 Å³
Envelope volume envelope_volume	62173 Å³
Hydration-shell volume shell_volume	24960 Å³
Envelope diameter envelope_diameter	66.9 Å
Shell Rg shell_rg	27.68 Å
Envelope Rg envelope_rg	20.30 Å
Shape Rg shape_rg	20.00 Å
Total Rg total_rg	21.01 Å
Total atoms total_atoms	3206
Residues n_residues	397
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	66.3 Å
Rg (real space) rg_real	21.07 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	3.4160e+07
I(0) uncertainty (real space) i0_real_error	4.0600e+05
Rg (reciprocal space) rg_reciprocal	21.10 Å
I(0) (reciprocal space) i0_reciprocal	34160000.0000
Solution quality estimate total_estimate	0.8960
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.3 Å
Skewness Skewness skewness	0.140
Kurtosis Kurtosis kurtosis	-0.413
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7537000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.887; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.995

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	NADPH dehydrogenase 1
Molecular weight formula_weight	44567.0 kDa
EC 编号 ec_number	1.6.99.1
Mutation mutation	W116A
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	3860

SFVKDFKPQALGDTNLFKPIKIGNNELLHRAVIPPLTRMRALHPGNIPNRDWAVEYYTQRAQRPGTMIITEGAFISPQAGGYDNAPGVWSEEQMVEWTKIFNAIHEKKSFVWVQLAVLGWAAFPDNLARDGLRYDSASDNVFMDAEQEAKAKKANNPQHSLTKDEIKQYIKEYVQAAKNSIAAGADGVEIHSANGYLLNQFLDPHSNTRTDEYGGSIENRARFTLEVVDALVEAIGHEKVGLRLSPYGVFNSMSGGAETGIVAQYAYVAGELEKRAKAGKRLAFVHLVEPRVTNPFLTEGEGEYEGGSNDFVYSIWKGPVIRAGNFALHPEVVREEVKDKRTLIGYGRFFISNPDLVDRLEKGLPLNKYDRDTFYQMSAHGYIDYPTYEEALKLGWD

来源 Source

来源生物 organism	Saccharomyces pastorianus
通用名 common_name	Lager yeast
NCBI Class编号 ncbi_taxonomy_id	27292
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	FLAVIN MONONUCLEOTIDE
Molecular weight formula_weight	456.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	methyl (2Z)-3-cyano-3-phenylprop-2-enoate
Molecular weight formula_weight	187.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	545

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ynca_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.4 — FMN-linked oxidoreductases
Family Family family	c.1.4.1 — FMN-linked oxidoreductases

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8. Citations (1)

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Unit-cell length a length_a	141.503 Å
Unit-cell length b length_b	141.503 Å
Unit-cell length c length_c	42.868 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	1.498 Å
Low-resolution limit resolution_low	27.751 Å
R factor r_factor	0.1559
R_work r_work	0.1554
R_free r_free	0.1725

fit	/app/data/saxs_computation/yn/4ync/4ync.fit
pddf	/app/data/pr_computation/yn/4ync/4ync.pr.out
profile	/app/data/saxs_computation/yn/4ync/4ync.dat