1lnl

Structure of deoxygenated hemocyanin from Rapana thomasiana

Method: X-RAY DIFFRACTION

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

hemocyanin

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	2-acetamido-2-deoxy-beta-D-glucopyranose × 6 COPPER (II) ION × 18	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HCY2E_RAPTH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–408； UniProt 7–413 Author chain B； PDBConstruct 2–408； UniProt 7–413 Author chain C； PDBConstruct 2–408； UniProt 7–413

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	1lnl
Deposition date deposition_date	2002-05-03
Structure title title	Structure of deoxygenated hemocyanin from Rapana thomasiana
Keywords keywords	hemocyanin, deoxygenated form, oxygen, metal binding site, cooperativity, OXYGEN STORAGE-TRANSPORT COMPLEX; OXYGEN STORAGE/TRANSPORT
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.

1lnl__assembly_1__model_1

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

Download this curve (.dat)

1lnl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1lnl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	44.89 Å
Rg (electron density)	44.23 Å
Total Rg	44.54 Å
Atom count	19968
Residues	2448
Excluded volume	350260 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1lnl__assembly_1__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	hemocyanin
Molecular weight formula_weight	46790.8 kDa
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	9984

GHRNLVRKSVRNLSPAERASLVAALKSLQEDSSADGFQSLASFHAQPPLCPAPAANKAFACCVHGMATFPEWHRLYTVQFEDALRRHGSVVGIPYWDTVVPQEDLPAFFNDEIWDDALFHANFTNPFNGADIDFNHQKIARDINVDKLAKEGPKGYDTWSFKQYIYALEQEDYCDFEVQFEIAHNAIHAWVGGTEEYSMGHLHYASYDPVFILHHSNTDRLFALWQELQKFRGHDPNEVNCALEMMREPLKPFSFGAPYNLNPTTKEHSKPEDTFDYKGHFHYEYDHLELQGMNVQRLHDYINQQKEADRVFAGFLLEGIGTSAHLDFSICAIDGECTHAGYFDVLGGSLETPWQFDRLYKYEITDVLESKGLDVHDVFDIKITQTSWDNEDISTDRFPPPSVIYVPK

Entity 2 Entity 2 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	3

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	9

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1lnla1
Class class	a — All alpha proteins
Fold Fold fold	a.86 — Di-copper centre-containing domain
Superfamily Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
Family Family family	a.86.1.1 — Hemocyanin middle domain

Domain ID domain_id	d1lnla2
Class class	b — All beta proteins
Fold Fold fold	b.112 — C-terminal domain of mollusc hemocyanin
Superfamily Superfamily superfamily	b.112.1 — C-terminal domain of mollusc hemocyanin
Family Family family	b.112.1.1 — C-terminal domain of mollusc hemocyanin

Domain ID domain_id	d1lnlb1
Class class	a — All alpha proteins
Fold Fold fold	a.86 — Di-copper centre-containing domain
Superfamily Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
Family Family family	a.86.1.1 — Hemocyanin middle domain

Domain ID domain_id	d1lnlb2
Class class	b — All beta proteins
Fold Fold fold	b.112 — C-terminal domain of mollusc hemocyanin
Superfamily Superfamily superfamily	b.112.1 — C-terminal domain of mollusc hemocyanin
Family Family family	b.112.1.1 — C-terminal domain of mollusc hemocyanin

Domain ID domain_id	d1lnlc1
Class class	a — All alpha proteins
Fold Fold fold	a.86 — Di-copper centre-containing domain
Superfamily Superfamily superfamily	a.86.1 — Di-copper centre-containing domain
Family Family family	a.86.1.1 — Hemocyanin middle domain

Domain ID domain_id	d1lnlc2
Class class	b — All beta proteins
Fold Fold fold	b.112 — C-terminal domain of mollusc hemocyanin
Superfamily Superfamily superfamily	b.112.1 — C-terminal domain of mollusc hemocyanin
Family Family family	b.112.1.1 — C-terminal domain of mollusc hemocyanin

CATH v4.4 (6 domains)

Domain ID domain_id	1lnlA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	1lnlA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	310 — Hemocyanin; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Haemocyanin C-terminal domain

Domain ID domain_id	1lnlB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	1lnlB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	310 — Hemocyanin; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Haemocyanin C-terminal domain

Domain ID domain_id	1lnlC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1280 — di-copper center containing domain from catechol oxidase
Homologous superfamily homologous superfamily	10 — Di-copper center containing domain from catechol oxidase

Domain ID domain_id	1lnlC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	310 — Hemocyanin; Chain: A, domain 2
Homologous superfamily homologous superfamily	10 — Haemocyanin C-terminal domain

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Unit-cell length a length_a	105.486 Å
Unit-cell length b length_b	105.486 Å
Unit-cell length c length_c	374.988 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	24

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2497
R_work r_work	0.2478
R_free r_free	0.2876

Structure of deoxygenated hemocyanin from Rapana thomasiana

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

hemocyanin

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

1lnl__assembly_1__model_1

1lnl__assembly_1__model_1 | I(q)

1lnl__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Structure of deoxygenated hemocyanin from Rapana thomasiana

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

hemocyanin

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

1lnl__assembly_1__model_1

1lnl__assembly_1__model_1 | I(q)

1lnl__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)