SAXSdb — 7cqd

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

Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964

Aquifex aeolicus VF5

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Heavy chain of antigen binding fragment, Fab of NZ-1 × 1 Light chain of antigen binding fragment, Fab of NZ-1 × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Heavy chain of antigen binding fragment, Fab of NZ-1 × 1 Light chain of antigen binding fragment, Fab of NZ-1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Y1964_AQUAE
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 3–123； UniProt 115–235 Author chain A； PDBConstruct 138–194； UniProt 236–292 Author chain B； PDBConstruct 3–123； UniProt 115–235 Author chain B； PDBConstruct 138–194； UniProt 236–292

Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964

Aquifex aeolicus VF5

UniProt Q86YL7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 3	Heavy chain of antigen binding fragment, Fab of NZ-1 × 1 Light chain of antigen binding fragment, Fab of NZ-1 × 1	Consistent with protein count
2	Insufficient information	Heteromer	Protein 3	Heavy chain of antigen binding fragment, Fab of NZ-1 × 1 Light chain of antigen binding fragment, Fab of NZ-1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PDPN_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 124–137； UniProt 38–51 Author chain B； PDBConstruct 124–137； UniProt 38–51

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	7cqd
Deposition date deposition_date	2020-08-10
Structure title title	The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236
Keywords keywords	soluble domain, Fab complex, MEMBRANE PROTEIN, HYDROLASE-IMMUNE SYSTEM complex; HYDROLASE/IMMUNE SYSTEM
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.

7cqd__assembly_2__model_1

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

Download this curve (.dat)

7cqd__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7cqd__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	28.89 Å
Rg (electron density)	28.93 Å
Total Rg	29.52 Å
Atom count	3951
Residues	519
Excluded volume	70147 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7cqd__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`7cqd__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Heavy chain of antigen binding fragment, Fab of NZ-1
Molecular weight formula_weight	23409.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,I
Atom count atom_count	7901

EVQLVESGGGLVQPGRSLKLSCAASGFTFSNYGMAWVRQTPTKGLEWIASISAGGDKTYYGDSVKGRFSISRDNAKTTHYLQMDSLRSEDTATYYCAKTSRVYFDYWGQGVMVTVSSAETTAPSVYPLAPGTALKSNSMVTLGCLVKGYFPEPVTVTWNSGALSSGVHTFPAVLQSGLYTLTSSVTVPSSTWSSQAVTCNVAHPASSTKVDKKIVPREC

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Mus musculus

Entity 2 Entity 2 polymer

Description description	Light chain of antigen binding fragment, Fab of NZ-1
Molecular weight formula_weight	23347.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M

QFVLTQPNSVSTNLGSTVKLSCKRSTGNIGSNYVNWYQQHEGRSPTTMIYRDDKRPDGVPDRFSGSIDRSSNSALLTINNVQTEDEADYFCHSYSSGIVFGGGTKLTVLGQPKSTPTLTVFPPSTEELQGNKATLVCLISDFYPSDVEVAWKANGAPISQGVDTANPTKQGNKYIASSFLRLTAEQWRSRNSFTCQVTHEGNTVEKSLSPAECV

Source Source

Source organism organism	Rattus norvegicus
Common name common_name	Norway rat
NCBI taxonomy ID ncbi_taxonomy_id	10116
Host organism host_organism	Mus musculus

Entity 3 Entity 3 polymer

Description description	Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964
Molecular weight formula_weight	21324.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

GSEVPKYLKEPVVVGYVQRDSIAQKIGIKPGDKIIKINGYEVRTWEDLRDALIRLSLDGVKETTLFLERNGEVLHLTIKVPNVQKGEELGIAPLVKPVVGGVKKGSPADQVGIKPGDLILEVNEGGVAMPGAEDDVVGKKINTWYELVEEVRKSQGKAIKLKILRNGKMIEKELIPAKDPKTGTYFIGLFPKTE

Source Source

Source organism organism	Aquifex aeolicus VF5
NCBI taxonomy ID ncbi_taxonomy_id	224324
Host organism host_organism	Escherichia coli

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	7cqdH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7cqdH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7cqdI01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	7cqdI02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	81.360 Å
Unit-cell length b length_b	80.175 Å
Unit-cell length c length_c	168.540 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	38.990 Å
R factor r_factor	0.2657
R_work r_work	0.2646
R_free r_free	0.2859

The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236

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

Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964

State in the Current Structure

Other States of the Same Protein in the Database

Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964

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

7cqd__assembly_2__model_1

7cqd__assembly_2__model_1 | I(q)

7cqd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

The NZ-1 Fab complexed with the PDZ tandem fragment of A. aeolicus S2P homolog with the PA14 tag inserted between the residues 235 and 236

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

Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Putative zinc metalloprotease aq_1964,PA14 from Podoplanin,Putative zinc metalloprotease aq_1964

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

7cqd__assembly_2__model_1

7cqd__assembly_2__model_1 | I(q)

7cqd__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)