SAXSdb — 4pit

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

Ripening-associated protein

Musa acuminata

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 3	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 3 alpha-D-mannopyranose × 1 GLYCEROL × 2 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 2	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose × 2 alpha-D-mannopyranose × 2 GLYCEROL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O22321_MUSAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–141； UniProt 1–141 Author chain B； PDBConstruct 1–141； UniProt 1–141 Author chain C； PDBConstruct 1–141； UniProt 1–141 Author chain D； PDBConstruct 1–141； UniProt 1–141

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	4pit
Deposition date deposition_date	2014-05-09
Structure title title	Crystal Structure of Banana Lectin H84T bound to dimannose
Keywords keywords	lectin, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
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.

4pit__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4pit__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4pit__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.72 Å
Rg (electron density)	19.53 Å
Total Rg	20.40 Å
Atom count	2129
Residues	284
Excluded volume	37936 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4pit__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4pit__assembly_2__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 (5)

Entity 1 Entity 1 polymer

Description description	Ripening-associated protein
Molecular weight formula_weight	15611.5 kDa
Mutation mutation	H84T
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4989

MNGAIKVGAWGGNGGSAFDMGPAYRIISVKIFSGDVVDGVDVTFTYYGKTETRHYGGSGGTPHEIVLQEGEYLVGMAGEVANYTGAVVLGKLGFSTNKKAYGPFGNTGGTPFSLPIAAGKISGFFGRGGKFLDAIGVYLEPLEHHHHHH

Source Source

Source organism organism	Musa acuminata
Common name common_name	Banana
NCBI taxonomy ID ncbi_taxonomy_id	4641
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	alpha-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	667

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4pita1
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.0 — automated matches

Domain ID domain_id	d4pita2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4pitb1
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.0 — automated matches

Domain ID domain_id	d4pitb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4pitc1
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.0 — automated matches

Domain ID domain_id	d4pitc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4pitd1
Class class	b — All beta proteins
Fold Fold fold	b.77 — beta-Prism I
Superfamily Superfamily superfamily	b.77.3 — Mannose-binding lectins
Family Family family	b.77.3.0 — automated matches

Domain ID domain_id	d4pitd2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (4 domains)

Domain ID domain_id	4pitA00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	4pitB00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	4pitC00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	4pitD00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

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Unit-cell length a length_a	50.613 Å
Unit-cell length b length_b	94.963 Å
Unit-cell length c length_c	63.054 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.550 Å
Low-resolution limit resolution_low	36.820 Å
R factor r_factor	0.1703
R_work r_work	0.1692
R_free r_free	0.1913

Crystal Structure of Banana Lectin H84T bound to dimannose

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

Ripening-associated protein

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

4pit__assembly_2__model_1

4pit__assembly_2__model_1 | I(q)

4pit__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of Banana Lectin H84T bound to dimannose

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

Ripening-associated protein

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

4pit__assembly_2__model_1

4pit__assembly_2__model_1 | I(q)

4pit__assembly_2__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (8 domains)

CATH v4.4 (4 domains)

7. Citations (1)