2w95

STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution

Method: X-RAY DIFFRACTION

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

DISCOIDIN-1 SUBUNIT A

DICTYOSTELIUM DISCOIDEUM

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	2-acetamido-2-deoxy-beta-D-galactopyranose × 3 (4S)-2-METHYL-2,4-PENTANEDIOL × 4 SULFATE ION × 7 CALCIUM ION × 3 (4R)-2-METHYLPENTANE-2,4-DIOL × 3 NICKEL (II) ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DIS1A_DICDI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–254； UniProt 1–253 Author chain B； PDBConstruct 2–254； UniProt 1–253 Author chain C； PDBConstruct 2–254； UniProt 1–253

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	2w95
Deposition date deposition_date	2009-01-21
Structure title title	STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution
Keywords keywords	CELL ADHESION, H TYPE LECTIN; CELL ADHESION
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.

2w95__assembly_1__model_1

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

Download this curve (.dat)

2w95__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2w95__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	31.07 Å
Rg (electron density)	30.20 Å
Total Rg	30.72 Å
Atom count	6115
Residues	760
Excluded volume	107580 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2w95__assembly_1__model_1`	trimeric （3）	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 (8)

Entity 1 Entity 1 polymer

Description description	DISCOIDIN-1 SUBUNIT A
Molecular weight formula_weight	28354.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	7173

AMSTQGLVQLLANAQCHLRTSTNYNGVHTQFNSALNYKNNGTNTIDGSEAWCSSIVDTNQYIVAGCEVPRTFMCVALQGRGDADQWVTSYKIRYSLDNVSWFEYRNGAAVTGVTDRNTVVNHFFDTPIRARSIAIHPLTWNGHISLRCEFYTQPVQSSVTQVGADIYTGDNCALNTGSGKREVVVPVKFQFEFATLPKVALNFDQIDCTDATNQTRIGVQPRNITTKGFDCVFYTWNENKVYSLRADYIATALE

Source Source

Source organism organism	DICTYOSTELIUM DISCOIDEUM
Common name common_name	SLIME MOLD
NCBI taxonomy ID ncbi_taxonomy_id	366501
Host organism host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-galactopyranose
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	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

Description description	(4R)-2-METHYLPENTANE-2,4-DIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	NICKEL (II) ION
Molecular weight formula_weight	58.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1053

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	2w95A01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2w95A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2080 —

Domain ID domain_id	2w95B01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2w95B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2080 —

Domain ID domain_id	2w95C01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	2w95C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	2080 —

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Unit-cell length a length_a	72.404 Å
Unit-cell length b length_b	274.047 Å
Unit-cell length c length_c	86.136 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	1.750 Å
Low-resolution limit resolution_low	47.400 Å
R factor r_factor	0.1590
R_work r_work	0.1570
R_free r_free	0.1930

STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution

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

DISCOIDIN-1 SUBUNIT A

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

2w95__assembly_1__model_1

2w95__assembly_1__model_1 | I(q)

2w95__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)

STructure of the Discoidin I from Dictyostelium discoideum in complex with GalNAc at 1.75 angstrom resolution

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

DISCOIDIN-1 SUBUNIT A

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

2w95__assembly_1__model_1

2w95__assembly_1__model_1 | I(q)

2w95__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 (8)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

7. Citations (1)