SAXSdb — 4m3k

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

Beta-lactamase

Bacillus licheniformis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Camelid heavy-chain antibody variable fragment cAb-H7S × 1 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BLAC_BACLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 44–307

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	4m3k
Deposition date deposition_date	2013-08-06
Structure title title	Structure of a single domain camelid antibody fragment cAb-H7S in complex with the BlaP beta-lactamase from Bacillus licheniformis
Keywords keywords	immunoglobulin fold, antigen binding, beta-lactamase-antibody complex, 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.

4m3k__assembly_1__model_1

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

Download this curve (.dat)

4m3k__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4m3k__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.49 Å
Rg (electron density)	21.56 Å
Total Rg	22.45 Å
Atom count	2892
Residues	376
Excluded volume	51261 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4m3k__assembly_1__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	Beta-lactamase
Molecular weight formula_weight	30412.3 kDa
EC 编号 ec_number	3.5.2.6
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	3224

TEMKDDFAKLEEQFDAKLGIFALDTGTNRTVAYRPDERFAFASTIKALTVGVLLQQKSIEDLNQRITYTRDDLVNYNPITEKHVDTGMTLKELADASLRYSDNAAQNLILKQIGGPESLKKELRKIGDEVTNPERFEPELNEVNPGETQDTSTARALVTSLRAFALEDPGKLPSEKRELLIDWMKRNTTGDALIRAGVPDGWEVADKTGAASYGTRNDIAIIWPPKGDPVVLAVLSSRDKKDAKYDDKLIAEATKVVMKALNMNGKGPHHHHH

Source Source

Source organism organism	Bacillus licheniformis
NCBI taxonomy ID ncbi_taxonomy_id	1402
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Camelid heavy-chain antibody variable fragment cAb-H7S
Molecular weight formula_weight	13524.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLQESGGGLVQPGGSLRLSCAASGSISSITTMGWYRQDPGKGRELVALINSVGDTTYAGSVKGRFTISRDNAKNTVYLEMSSLKPEDTAVYYCNAFMSTNSGRTGSFWGQGTQVTVSSHHHHHH

Source Source

Source organism organism	Lama glama
NCBI taxonomy ID ncbi_taxonomy_id	9844
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d4m3ka_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d4m3kb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d4m3kb2
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 (2 domains)

Domain ID domain_id	4m3kA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	4m3kB00
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	51.818 Å
Unit-cell length b length_b	42.940 Å
Unit-cell length c length_c	74.818 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.29 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.480 Å
Low-resolution limit resolution_low	36.900 Å
R factor r_factor	0.1629
R_work r_work	0.1612
R_free r_free	0.1947

Structure of a single domain camelid antibody fragment cAb-H7S in complex with the BlaP beta-lactamase from Bacillus licheniformis

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

Beta-lactamase

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

4m3k__assembly_1__model_1

4m3k__assembly_1__model_1 | I(q)

4m3k__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Structure of a single domain camelid antibody fragment cAb-H7S in complex with the BlaP beta-lactamase from Bacillus licheniformis

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

Beta-lactamase

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

4m3k__assembly_1__model_1

4m3k__assembly_1__model_1 | I(q)

4m3k__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

7. Citations (1)