1zhq

Crystal structure of apo MVL

Method: X-RAY DIFFRACTION

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

mannan-binding lectin

Microcystis viridis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 4 1,2-ETHANEDIOL × 5 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 1 1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 1 1,2-ETHANEDIOL × 4 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9RHG4_9CHRO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–113； UniProt 2–114 Author chain B； PDBConstruct 1–113； UniProt 2–114 Author chain C； PDBConstruct 1–113； UniProt 2–114 Author chain D； PDBConstruct 1–113； UniProt 2–114 Author chain E； PDBConstruct 1–113； UniProt 2–114 Author chain F； PDBConstruct 1–113； UniProt 2–114 Author chain G； PDBConstruct 1–113； UniProt 2–114 Author chain H； PDBConstruct 1–113； UniProt 2–114

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	1zhq
Deposition date deposition_date	2005-04-26
Structure title title	Crystal structure of apo MVL
Keywords keywords	HIV-1, MVL, cyanobacteria, carbohydrate binding, 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.

1zhq__assembly_1__model_1

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

Download this curve (.dat)

1zhq__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zhq__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	18.04 Å
Rg (electron density)	16.73 Å
Total Rg	17.73 Å
Atom count	1770
Residues	226
Excluded volume	31272 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zhq__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zhq__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1zhq__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1zhq__assembly_4__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 (4)

Entity 1 Entity 1 polymer

Description description	mannan-binding lectin
Molecular weight formula_weight	12244.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	7867

ASYKVNIPAGPLWSNAEAQQVGPKIAAAHQGNFTGQWTTVVESAMSVVEVELQVENTGIHEFKTDVLAGPLWSNDEAQKLGPQIAASYGAEFTGQWRTIVEGVMSVIQIKYTF

Source Source

Source organism organism	Microcystis viridis
NCBI taxonomy ID ncbi_taxonomy_id	44822
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	865

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1zhqa1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqa2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqd1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqd2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqe1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqe2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqf1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqf2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqg1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqg2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqh1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

Domain ID domain_id	d1zhqh2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.7 — Oligosaccharide binding protein
Family Family family	d.230.7.1 — Oligomannose binding protein MVL-like

CATH v4.4 (16 domains)

Domain ID domain_id	1zhqA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqE02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqF01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqF02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqG01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqG02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqH01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	1zhqH02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	230 —

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Unit-cell length a length_a	76.184 Å
Unit-cell length b length_b	74.873 Å
Unit-cell length c length_c	83.901 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

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

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	19.870 Å
R factor r_factor	0.1770
R_work r_work	0.1770
R_free r_free	0.2160

Crystal structure of apo MVL

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

mannan-binding lectin

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

1zhq__assembly_1__model_1

1zhq__assembly_1__model_1 | I(q)

1zhq__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 (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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Crystal structure of apo MVL

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

mannan-binding lectin

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

1zhq__assembly_1__model_1

1zhq__assembly_1__model_1 | I(q)

1zhq__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 (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) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)