1w7c

PPLO at 1.23 Angstroms

Method: X-RAY DIFFRACTION

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

LYSYL OXIDASE

PICHIA PASTORIS

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 COPPER (II) ION × 2 CALCIUM ION × 4 MAGNESIUM ION × 10 CHLORIDE ION × 10 IMIDAZOLE × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96X16_PICPA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–747； UniProt 41–787

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1w7c
Deposition date deposition_date	2004-09-01
Structure title title	PPLO at 1.23 Angstroms
Keywords keywords	AMINE OXIDASE, OXIDOREDUCTASE, QUINOPROTEIN, TOPAQUINONE ENZYME; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

1w7c__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1w7c__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1w7c__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	34.94 Å
Rg (electron density)	34.26 Å
Total Rg	34.88 Å
Atom count	22452
Residues	1472
Excluded volume	212290 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1w7c__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	LYSYL OXIDASE
Molecular weight formula_weight	85289.1 kDa
EC 编号 ec_number	1.4.3.13
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	12713

ASAECVSNENVEIEAPKTNIWTSLAKEEVQEVLDLLHSTYNITEVTKADFFSNYVLWIETLKPNKTEALTYLDEDGDLPPRNARTVVYFGEGEEGYFEELKVGPLPVSDETTIEPLSFYNTNGKSKLPFEVGHLDRIKSAAKSSFLNKNLNTTIMRDVLEGLIGVPYEDMGCHSAAPQLHDPATGATVDYGTCNINTENDAENLVPTGFFFKFDMTGRDVSQWKMLEYIYNNKVYTSAEELYEAMQKDDFVTLPKIDVDNLDWTVIQRNDSAPVRHLDDRKSPRLVEPEGRRWAYDGDEEYFSWMDWGFYTSWSRDTGISFYDITFKGERIVYELSLQELIAEYGSDDPFNQHTFYSDISYGVGNRFSLVPGYDCPSTAGYFTTDTFEYDEFYNRTLSYCVFENQEDYSLLRHTGASYSAITQNPTLNVRFISTIGNYDYNFLYKFFLDGTLEVSVRAAGYIQAGYWNPETSAPYGLKIHDVLSGSFHDHVLNYKVDLDVGGTKNRASQYVMKDVDVEYPWAPGTVYNTKQIAREVFENEDFNGINWPENGQGILLIESAEETNSFGNPRAYNIMPGGGGVHRIVKNSRSGPETQNWARSNLFLTKHKDTELRSSTALNTNALYDPPVNFNAFLDDESLDGEDIVAWVNLGLHHLPNSNDLPNTIFSTAHASFMLTPFNYFDSENSRDTTQQVFYTYDDETEESNWEFYGNDWSSCGVEVAEPNFEDYTYGRGTRINKKMTNSDEVY

Source Source

Source organism organism	PICHIA PASTORIS
NCBI taxonomy ID ncbi_taxonomy_id	4922
Host organism host_organism	PICHIA PASTORIS

Entity 2 Entity 2 branched

Description description	beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	586.5 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 7 Entity 7 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1046

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6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1w7ca1
Class class	b — All beta proteins
Fold Fold fold	b.30 — Supersandwich
Superfamily Superfamily superfamily	b.30.2 — Amine oxidase catalytic domain
Family Family family	b.30.2.1 — Amine oxidase catalytic domain

Domain ID domain_id	d1w7ca2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

Domain ID domain_id	d1w7ca3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.17 — Cystatin-like
Superfamily Superfamily superfamily	d.17.2 — Amine oxidase N-terminal region
Family Family family	d.17.2.1 — Amine oxidase N-terminal region

CATH v4.4 (3 domains)

Domain ID domain_id	1w7cA01
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	20 — Copper amine oxidase, catalytic domain

Domain ID domain_id	1w7cA02
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1w7cA03
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	450 — Nuclear Transport Factor 2; Chain: A,
Homologous superfamily homologous superfamily	40 —

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Unit-cell length a length_a	139.948 Å
Unit-cell length b length_b	67.027 Å
Unit-cell length c length_c	108.688 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	118.95 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.230 Å
Low-resolution limit resolution_low	24.010 Å
R factor r_factor	0.1130
R_work r_work	0.1120
R_free r_free	0.1460

PPLO at 1.23 Angstroms

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

LYSYL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1w7c__assembly_1__model_1

1w7c__assembly_1__model_1 | I(q)

1w7c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)

PPLO at 1.23 Angstroms

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

LYSYL OXIDASE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

1w7c__assembly_1__model_1

1w7c__assembly_1__model_1 | I(q)

1w7c__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (3 domains)

CATH v4.4 (3 domains)

7. Citations (1)