SAXSdb — 2fam

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

MYOGLOBIN

Aplysia limacina

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	THIOCYANATE ION × 1 PROTOPORPHYRIN IX CONTAINING FE × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLB_APLLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–147； UniProt 1–146

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	2fam
Deposition date deposition_date	1993-07-20
Structure title title	X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES
Keywords keywords	OXYGEN STORAGE; OXYGEN STORAGE
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.

2fam__assembly_1__model_1

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

Download this curve (.dat)

2fam__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2fam__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.75 Å
Rg (electron density)	14.32 Å
Total Rg	15.61 Å
Atom count	1132
Residues	146
Excluded volume	20232 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2fam__assembly_1__model_1`	monomeric （1）	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 (4)

Entity 1 Entity 1 polymer

Description description	MYOGLOBIN
Molecular weight formula_weight	15407.5 kDa
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	1225

XSLSAAEADLAGKSWAPVFANKNANGLDFLVALFEKFPDSANFFADFKGKSVADIKASPKLRDVSSRIFTRLNEFVNNAANAGKMSAMLSQFAKEHVGFGVGSAQFENVRSMFPGFVASVAAPPAGADAAWTKLFGLIIDALKAAGK

Source Source

Source organism organism	Aplysia limacina
Common name common_name	slug sea hare
NCBI taxonomy ID ncbi_taxonomy_id	6502

Entity 2 Entity 2 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	PROTOPORPHYRIN IX CONTAINING FE
Molecular weight formula_weight	616.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2fama_
Class class	a — All alpha proteins
Fold Fold fold	a.1 — Globin-like
Superfamily Superfamily superfamily	a.1.1 — Globin-like
Family Family family	a.1.1.2 — Globins

CATH v4.4 (1 domains)

Domain ID domain_id	2famA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	490 — Globin-like
Homologous superfamily homologous superfamily	10 — Globins

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7. Citations (7)

X-ray crystal structure of ferric Aplysia limacina myoglobin in different liganded states.

J.Mol.Biol. (1993)

PMID: 8411158 · DOI: 10.1006/jmbi.1993.1527 PRIMARY

X-Ray Crystal Structure of the Ferric Sperm Whale Myoglobin: Imidazole Complex at 2.0 Angstroms Resolution

J.Mol.Biol. (1991)

Aplysia Limacina Myoglobin: Molecular Bases for Ligand Binding

Structure and Function of Invertebrate Oxygen Carriers (1991)

Binding Mode of Azide to Ferric Aplysia Limacina Myoglobin: Crystallographic Analysis at 1.9 Angstroms Resolution

J.Mol.Recog. (1991)

;X-Ray Crystal Structure of the Fluoride Derivative of Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution: Stabilization of the Fluoride by Hydrogen Bonding to Arg66 (E10) ;

J.Mol.Biol. (1990)

Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution

J.Mol.Biol. (1989)

Reactivity of Ferric Aplysia and Sperm Whale Myoglobins Towards Imidazole. X-Ray and Binding Study

J.Mol.Biol. (1982)

Unit-cell length a length_a	52.980 Å
Unit-cell length b length_b	70.700 Å
Unit-cell length c length_c	32.500 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1610
R_work r_work	—
R_free r_free	—

X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES

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

MYOGLOBIN

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

2fam__assembly_1__model_1

2fam__assembly_1__model_1 | I(q)

2fam__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (7)

X-RAY CRYSTAL STRUCTURE OF FERRIC APLYSIA LIMACINA MYOGLOBIN IN DIFFERENT LIGANDED STATES

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

MYOGLOBIN

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

2fam__assembly_1__model_1

2fam__assembly_1__model_1 | I(q)

2fam__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

7. Citations (7)