SAXSdb — 5mba

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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	AZIDE 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 2–146； UniProt 1–145

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	5mba
Deposition date deposition_date	1991-01-14
Structure title title	BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION
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.

5mba__assembly_1__model_1

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

Download this curve (.dat)

5mba__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5mba__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	15.63 Å
Rg (electron density)	14.26 Å
Total Rg	15.53 Å
Atom count	1132
Residues	146
Excluded volume	20206 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5mba__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	15349.4 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	1258

XSLSAAEADLAGKSWAPVFANKNANGLDFLVALFEKFPDSANFFADFKGKSVADIKASPKLRDVSSRIFTRLNEFVNNAANAGKMSAMLSQFAKEHVGFGVGSAQFENVRSMFPGFVASVAAPPAGADAAWTKLFGLIIDALKAAGA

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	AZIDE ION
Molecular weight formula_weight	42.0 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	126

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5mbaa_
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	5mbaA00
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 (9)

Binding mode of azide to ferric Aplysia limacina myoglobin. Crystallographic analysis at 1.9 A resolution.

J.Mol.Recog. (1991)

PMID: 1931125 · DOI: 10.1002/jmr.300040102 PRIMARY

Aplysia Limacina Myoglobin: Molecular Bases for Ligand Binding

Structure and Function of Invertebrate Oxygen Carriers (1991)

Aplysia Limacina Myoglobin. Crystallographic Analysis at 1.6 Angstroms Resolution

J.Mol.Biol. (1989)

Crystal Structure of Ferric Aplysia Limacina Myoglobin at 2.0 Angstroms Resolution

J.Mol.Biol. (1985)

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

J.Mol.Biol. (1982)

The Structure of Aplysia Limacina Myoglobin at 3.6 Angstroms Resolution

Acta Crystallogr.,Sect.A (Supplement) (1978)

The Crystal Structure of met-Myoglobin from Aplysia Limacina at 5 Angstroms Resolution

Acta Crystallogr.,Sect.B (1978)

Crystallization and Preliminary X-Ray Diffraction Studies on met-Myoglobin from Aplysia Limacina

J.Mol.Biol. (1975)

The Amino Acid Sequence of Myoglobin from the Mollusc Aplysia Limacina

Int.J.Pept.Protein Res. (1973)

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	1.900 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	0.1390
R_work r_work	—
R_free r_free	—

BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION

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

5mba__assembly_1__model_1

5mba__assembly_1__model_1 | I(q)

5mba__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 (9)

BINDING MODE OF AZIDE TO FERRIC APLYSIA LIMACINA MYOGLOBIN. CRYSTALLOGRAPHIC ANALYSIS AT 1.9 ANGSTROMS RESOLUTION

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

5mba__assembly_1__model_1

5mba__assembly_1__model_1 | I(q)

5mba__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 (9)