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1e8h

STRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN THE APO FORM COMPLEXED BY ADP

Method: X-RAY DIFFRACTION Dmax: 94.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

VANILLYL-ALCOHOL OXIDASE

PENICILLIUM SIMPLICISSIMUM

UniProt P56216

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 homooligomer Homooligomer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–560 Chain B； UniProt 1–560 Mutation：YES ADP ADENOSINE-5'-DIPHOSPHATE × 8 X-RAY DIFFRACTION X-ray crystallization conditions：pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6 Resolution 2.60 Å R-free 0.303

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 1E8H Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AHU STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH P-CRESOL Deposited 1997-04-10 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded FAA N5-(4-HYDROXYBENZYL)FLAVIN-ADENINE DINUCLEOTIDE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.70 Å R-free 0.290
1AHV STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH 2-NITRO-P-CRESOL Deposited 1997-04-10 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 NCR 2-NITRO-P-CRESOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 3.10 Å R-free 0.240
1AHV STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH 2-NITRO-P-CRESOL Deposited 1997-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 NCR 2-NITRO-P-CRESOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 3.10 Å R-free 0.240
1AHZ STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH 4-(1-HEPTENYL)PHENOL Deposited 1997-04-10 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded CL CHLORIDE ION × 8 FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 EPT HEPTANYL-P-PHENOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 3.30 Å R-free 0.260
1AHZ STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH 4-(1-HEPTENYL)PHENOL Deposited 1997-04-10 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded CL CHLORIDE ION × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 EPT HEPTANYL-P-PHENOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 3.30 Å R-free 0.260
1DZN Asp170Ser mutant of vanillyl-alcohol oxidase Deposited 2000-03-05 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.60
Resolution 2.80 Å R-free 0.291
1E0Y Structure of the D170S/T457E double mutant of vanillyl-alcohol oxidase Deposited 2000-04-11 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 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 FCR ALPHA,ALPHA,ALPHA-TRIFLUORO-P-CRESOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.60
Resolution 2.75 Å R-free 0.287
1E8F STRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN THE APO FORM Deposited 2000-09-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 100 MM ACETATE BUFFER PH 4.6, 6% PEG4000
Resolution 2.90 Å R-free 0.312
1E8G STRUCTURE OF THE H61T DOUBLE MUTANT OF VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH FLUORO-CRESOL Deposited 2000-09-20 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 FCR ALPHA,ALPHA,ALPHA-TRIFLUORO-P-CRESOL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.60
Resolution 2.10 Å R-free 0.258
1QLT STRUCTURE OF THE H422A MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE Deposited 1999-09-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 ACT ACETATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.20 Å R-free 0.264
1QLU STRUCTURE OF THE H422A MUTANT VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH ISOEUGENOL Deposited 1999-09-16 Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.40 Å R-free 0.273
1VAO STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE Deposited 1997-04-10 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded ACT ACETATE ION × 8 CL CHLORIDE ION × 8 FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.50 Å R-free 0.290
1W1J STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: The505Ser Mutant Deposited 2004-06-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.70 Å R-free 0.292
1W1K STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Ile238Thr Mutant Deposited 2004-06-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.55 Å R-free 0.272
1W1L STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Phe454Tyr Mutant Deposited 2004-06-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.70 Å R-free 0.293
1W1M STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE: Glu502Gly Mutant Deposited 2004-06-22 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Mutation：YES Mutation：YES FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 3.00 Å R-free 0.307
2VAO STRUCTURE OF THE OCTAMERIC FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH ISOEUGENOL Deposited 1997-04-10 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 8 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；FROM 6% PEG4000, 100 MM ACETATE BUFFER PH 4.6
Resolution 2.80 Å R-free 0.290
5MXJ Structure of the Y108F mutant of vanillyl alcohol oxidase Deposited 2017-01-23 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 GOL GLYCEROL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；PEG4000, sodium acetate
Resolution 2.80 Å R-free 0.259
5MXU Structure of the Y503F mutant of vanillyl alcohol oxidase Deposited 2017-01-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric
Chain A 1–560（560 aa）
Chain B 1–560（560 aa）
Not recorded FAD FLAVIN-ADENINE DINUCLEOTIDE × 8 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；PEG4000, sodium acetate
Resolution 2.80 Å R-free 0.249

17 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name VAOX_PENSI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–560； UniProt 1–560 Author chain B； PDBConstruct 1–560； UniProt 1–560

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 1e8h

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1e8h
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1e8h
Deposition date deposition_date2000-09-20
Structure title titleSTRUCTURE OF THE H61T MUTANT OF THE FLAVOENZYME VANILLYL-ALCOHOL OXIDASE IN THE APO FORM COMPLEXED BY ADP
Keywords keywordsOXIDOREDUCTASE, FLAVOPROTEIN, METHANOL UTILIZATION, PEROXISOME, FLAVOENZYME, OXIDASE, CATALYSIS; OXIDOREDUCTASE
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_guinier30.45 Å
Radius of gyration Rg (electron density) rg_electron29.58 Å
Forward intensity I(0) i0231047000.00
Molecular weight molecular_weight123150.0 kDa
Excluded volume excluded_volume154680 ų
Envelope volume envelope_volume181320 ų
Hydration-shell volume shell_volume48588 ų
Envelope diameter envelope_diameter99.9 Å
Shell Rg shell_rg38.78 Å
Envelope Rg envelope_rg29.83 Å
Shape Rg shape_rg29.57 Å
Total Rg total_rg30.36 Å
Total atoms total_atoms8676
Residues n_residues1090
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 dmax94.4 Å
Rg (real space) rg_real30.30 Å
Rg uncertainty (real space) rg_real_error0.49 Å
I(0) (real space) i0_real2.3100e+08
I(0) uncertainty (real space) i0_real_error3.3830e+06
Rg (reciprocal space) rg_reciprocal30.37 Å
I(0) (reciprocal space) i0_reciprocal231100000.0000
Solution quality estimate total_estimate0.8970
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.1 Å
Skewness Skewness skewness0.215
Kurtosis Kurtosis kurtosis-0.396
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha115700000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.913; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.929
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1e8ha1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.32 — FAD-linked oxidases, C-terminal domain
Family Family familyd.58.32.1 — Vanillyl-alcohol oxidase-like
Domain ID domain_idd1e8ha2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
Family Family familyd.145.1.1 — FAD-linked oxidases, N-terminal domain
Domain ID domain_idd1e8hb1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.58 — Ferredoxin-like
Superfamily Superfamily superfamilyd.58.32 — FAD-linked oxidases, C-terminal domain
Family Family familyd.58.32.1 — Vanillyl-alcohol oxidase-like
Domain ID domain_idd1e8hb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.145 — FAD-binding/transporter-associated domain-like
Superfamily Superfamily superfamilyd.145.1 — FAD-binding/transporter-associated domain-like
Family Family familyd.145.1.1 — FAD-linked oxidases, N-terminal domain

CATH v4.4 (8 domains)

Domain ID domain_id1e8hA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
Domain ID domain_id1e8hA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1e8hA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — FAD-linked oxidases, C-terminal domain
Domain ID domain_id1e8hA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology45 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Homologous superfamily homologous superfamily10 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Domain ID domain_id1e8hB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology43 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2
Homologous superfamily homologous superfamily10 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2
Domain ID domain_id1e8hB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology465 — Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3
Homologous superfamily homologous superfamily10 —
Domain ID domain_id1e8hB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology462 — Vanillyl-alcohol Oxidase; Chain A, domain 3
Homologous superfamily homologous superfamily10 — FAD-linked oxidases, C-terminal domain
Domain ID domain_id1e8hB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology45 — Vanillyl-alcohol Oxidase; Chain A, domain 4
Homologous superfamily homologous superfamily10 — Vanillyl-alcohol Oxidase; Chain A, domain 4
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8. Citations (1)

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9. Files and Curves (10)