SAXSdb — 6y6j

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

Metallo-beta-lactamase VIM-2

Pseudomonas aeruginosa

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	Biapenem Imine hydrolysis product × 1 Biapenem Enamine hydrolysis product × 1 ZINC ION × 3 CHLORIDE ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D1MEN9_PSEAI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–232； UniProt 32–263

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	6y6j
Deposition date deposition_date	2020-02-26
Structure title title	VIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products
Keywords keywords	Metallo beta lactamases, VIM2, biapenem, enzyme product complex, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL 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.

6y6j__assembly_1__model_1

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

Download this curve (.dat)

6y6j__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6y6j__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.09 Å
Rg (electron density)	15.87 Å
Total Rg	16.91 Å
Atom count	1758
Residues	232
Excluded volume	31020 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6y6j__assembly_1__model_1`	monomeric （1）	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	Metallo-beta-lactamase VIM-2
Molecular weight formula_weight	24766.5 kDa
Mutation mutation	0
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	2048

EYPTVSEIPVGEVRLYQIADGVWSHIATQSFDGAVYPSNGLIVRDGDELLLIDTAWGAKNTAALLAEIEKQIGLPVTRAVSTHFHDDRVGGVDVLRAAGVATYASPSTRRLAEVEGNEIPTHSLEGLSSSGDAVRFGPVELFYPGAAHSTDNLVVYVPSASVLYGGCAIYELSRTSAGNVADADLAEWPTSIERIQQHYPEAQFVIPGHGLPGGLDLLKHTTNVVKAHTNRS

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	Biapenem Imine hydrolysis product
Molecular weight formula_weight	369.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	Biapenem Enamine hydrolysis product
Molecular weight formula_weight	369.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	3

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	3

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	196

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6. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6y6ja_
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

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Unit-cell length a length_a	64.324 Å
Unit-cell length b length_b	74.020 Å
Unit-cell length c length_c	78.354 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	27.610 Å
R factor r_factor	0.1302
R_work r_work	0.1287
R_free r_free	0.1573

VIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products

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

Metallo-beta-lactamase VIM-2

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

6y6j__assembly_1__model_1

6y6j__assembly_1__model_1 | I(q)

6y6j__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) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)

VIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products

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

Metallo-beta-lactamase VIM-2

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

6y6j__assembly_1__model_1

6y6j__assembly_1__model_1 | I(q)

6y6j__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) 1 domains

SCOP 2.08 (1 domains)

7. Citations (1)