SAXSdb — 5dpx

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

Metallo-beta-lactamase L1 type 3

Stenotrophomonas maltophilia

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	ZINC ION × 8 5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione × 4 SULFATE ION × 8 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BLA1_STEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–269； UniProt 22–290 Author chain B； PDBConstruct 1–269； UniProt 22–290

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	5dpx
Deposition date deposition_date	2015-09-14
Structure title title	1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.
Keywords keywords	HYDROLASE, METALLO, ZN, LACTAMASE; HYDROLASE
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.

5dpx__assembly_1__model_1

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

Download this curve (.dat)

5dpx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dpx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.58 Å
Rg (electron density)	29.49 Å
Total Rg	30.25 Å
Atom count	8132
Residues	1064
Excluded volume	142770 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dpx__assembly_1__model_1`	tetrameric （4）	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	Metallo-beta-lactamase L1 type 3
Molecular weight formula_weight	28740.5 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4661

AEVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAGAR

Source Source

Source organism organism	Stenotrophomonas maltophilia
Common name common_name	Pseudomonas maltophilia
NCBI taxonomy ID ncbi_taxonomy_id	40324
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	5-(2-methylphenyl)-3H-1,2,4-triazole-3-thione
Molecular weight formula_weight	189.2 kDa
Source method src_method	syn
Copy count entity_count	2

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	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	518

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5dpxa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.1 — Zn metallo-beta-lactamase

Domain ID domain_id	d5dpxb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.157 — Metallo-hydrolase/oxidoreductase
Superfamily Superfamily superfamily	d.157.1 — Metallo-hydrolase/oxidoreductase
Family Family family	d.157.1.1 — Zn metallo-beta-lactamase

CATH v4.4 (2 domains)

Domain ID domain_id	5dpxA00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Domain ID domain_id	5dpxB00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	15 — Metallo-beta-lactamase; Chain A
Homologous superfamily homologous superfamily	10 — Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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Unit-cell length a length_a	105.040 Å
Unit-cell length b length_b	105.040 Å
Unit-cell length c length_c	196.990 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 62 2 2
Space-group number int_tables_number	180
Crystal system crystal_system	—

Resolution resolution	1.850 Å
Low-resolution limit resolution_low	19.851 Å
R factor r_factor	0.1684
R_work r_work	0.1670
R_free r_free	0.2066

1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.

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

Metallo-beta-lactamase L1 type 3

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

5dpx__assembly_1__model_1

5dpx__assembly_1__model_1 | I(q)

5dpx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)

1,2,4-Triazole-3-thione compounds as inhibitors of L1, di-zinc metallo-beta-lactamases.

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

Metallo-beta-lactamase L1 type 3

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

5dpx__assembly_1__model_1

5dpx__assembly_1__model_1 | I(q)

5dpx__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 (5)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (4)