1w4n

AGAO covalent complex with Tranylcypromine

Method: X-RAY DIFFRACTION Dmax: 106.9 Å Quality: REASONABLE

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

PHENYLETHYLAMINE OXIDASE

ARTHROBACTER GLOBIFORMIS

UniProt P46881

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 3–638 Chain B; UniProt 3–638 Non-standard monomer:Yes (specific site not provided by mmCIF) CU COPPER (II) ION × 2 NA SODIUM ION × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 9 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;293 K;AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A SINGLE CRYSTAL WAS SOAKED WITH TCP BY SLOWLY ADDING TCP TO THE DROP TO ACHIEVE A 100 FOLD EXCESS OF TCP OVER ENZYME ACTIVE SITES. THE CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL, WITH THE CONCENTRAION OF TCP BEING MAINTAINED CONSTANT. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. Resolution 1.65 Å R-free 0.199

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.

105 other PDB entries and 143 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAOX_ARTGO
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–636; UniProt 3–638 Author chain B; PDBConstruct 1–636; UniProt 3–638

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 1w4n

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1w4n
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1w4n
Deposition date deposition_date2004-07-27
Structure title titleAGAO covalent complex with Tranylcypromine
Keywords keywords;AMINE OXIDASE, ARTHROBACTER GLOBIFORMIS, COPPER CONTAINING, METAL-BINDING, OXIDOREDUCTASE, TCQ, QUINONE, INHIBITED, TCP, TRANYLCYPROMINE ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier32.52
Radius of gyration Rg (electron density) rg_electron31.67
Forward intensity I(0) i0305230000.00
Molecular weight molecular_weight138790.0 kDa
Excluded volume excluded_volume172630 ų
Envelope volume envelope_volume204460 ų
Hydration-shell volume shell_volume51846 ų
Envelope diameter envelope_diameter114.6
Shell Rg shell_rg40.19
Envelope Rg envelope_rg31.94
Shape Rg shape_rg31.65
Total Rg total_rg32.36
Total atoms total_atoms18791
Residues n_residues1236
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax106.9
Rg (real space) rg_real32.44
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real3.0520e+08
I(0) uncertainty (real space) i0_real_error5.0030e+06
Rg (reciprocal space) rg_reciprocal32.47
I(0) (reciprocal space) i0_reciprocal305200000.0000
Solution quality estimate total_estimate0.6666
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.3
Skewness Skewness skewness0.346
Kurtosis Kurtosis kurtosis-0.228
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha92520000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.829; Stabil: 1.000; Sysdev: 0.096; Positv: 1.000; Valcen: 0.998; Smooth: 0.888

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1w4na1
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
Family Family familyb.30.2.1 — Amine oxidase catalytic domain
Domain ID domain_idd1w4na2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region
Domain ID domain_idd1w4na3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region
Domain ID domain_idd1w4nb1
Class classb — All beta proteins
Fold Fold foldb.30 — Supersandwich
Superfamily Superfamily superfamilyb.30.2 — Amine oxidase catalytic domain
Family Family familyb.30.2.1 — Amine oxidase catalytic domain
Domain ID domain_idd1w4nb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region
Domain ID domain_idd1w4nb3
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.17 — Cystatin-like
Superfamily Superfamily superfamilyd.17.2 — Amine oxidase N-terminal region
Family Family familyd.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (6 domains)

Domain ID domain_id1w4nA01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1w4nA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1w4nA03
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain
Domain ID domain_id1w4nB01
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1w4nB02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily40
Domain ID domain_id1w4nB03
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily20 — Copper amine oxidase, catalytic domain

8. Citations (1)

9. Files and Curves (10)