SAXSdb — 5acx

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

BETA-LACTAMASE

PSEUDOMONAS AERUGINOSA

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	ZINC ION × 6 2-(4-fluorophenyl)carbonylbenzoic acid × 2 HYDROXIDE ION × 2 CHLORIDE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9K2N0_PSEAI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–266； UniProt 1–266 Author chain B； PDBConstruct 1–266； UniProt 1–266

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	5acx
Deposition date deposition_date	2015-08-18
Structure title title	VIM-2-2, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening
Keywords keywords	HYDROLASE; 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.

5acx__assembly_1__model_1

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

Download this curve (.dat)

5acx__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5acx__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.28 Å
Rg (electron density)	24.58 Å
Total Rg	25.47 Å
Atom count	6953
Residues	463
Excluded volume	62577 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5acx__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 (6)

Entity 1 Entity 1 polymer

Description description	BETA-LACTAMASE
Molecular weight formula_weight	28400.8 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	7942

MFKLLSKLLVYLTASIMAIASPLAFSVDSSGEYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRSVVE

Source Source

Source organism organism	PSEUDOMONAS AERUGINOSA
NCBI taxonomy ID ncbi_taxonomy_id	287
Host organism host_organism	ESCHERICHIA COLI

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	6

Entity 3 Entity 3 non-polymer

Description description	2-(4-fluorophenyl)carbonylbenzoic acid
Molecular weight formula_weight	244.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	HYDROXIDE ION
Molecular weight formula_weight	17.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	616

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5acxa_
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	d5acxb_
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	5acxA00
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	5acxB00
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	101.230 Å
Unit-cell length b length_b	79.220 Å
Unit-cell length c length_c	67.640 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	130.18 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	39.610 Å
R factor r_factor	0.1474
R_work r_work	0.1451
R_free r_free	0.1925

VIM-2-2, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening

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

5acx__assembly_1__model_1

5acx__assembly_1__model_1 | I(q)

5acx__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

VIM-2-2, Discovery of novel inhibitor scaffolds against the metallo- beta-lactamase VIM-2 by SPR based fragment screening

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

5acx__assembly_1__model_1

5acx__assembly_1__model_1 | I(q)

5acx__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 (6)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)