SAXSdb — 6zys

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

Beta-lactamase IMP-1

Serratia marcescens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 2 (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid × 1 1,2-ETHANEDIOL × 2 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid × 1 1,2-ETHANEDIOL × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BLAB_SERMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–230； UniProt 19–246 Author chain B； PDBConstruct 3–230； UniProt 19–246 Author chain C； PDBConstruct 3–230； UniProt 19–246 Author chain D； PDBConstruct 3–230； UniProt 19–246

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	6zys
Deposition date deposition_date	2020-08-02
Structure title title	Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b
Keywords keywords	antibiotic resistance, lactamase, zinc, inhibitor, 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.

6zys__assembly_1__model_1

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

Download this curve (.dat)

6zys__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6zys__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	17.46 Å
Rg (electron density)	16.37 Å
Total Rg	17.47 Å
Atom count	1731
Residues	219
Excluded volume	31192 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6zys__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6zys__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6zys__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6zys__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	Beta-lactamase IMP-1
Molecular weight formula_weight	25300.8 kDa
EC 编号 ec_number	3.5.2.6
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7450

GPAESLPDLKIEKLDEGVYVHTSFEEVNGWGVVPKHGLVVLVNAEAYLIDTPFTAKDTEKLVTWFVERGYKIKGSISSHFHSDSTGGIEWLNSRSIPTYASELTNELLKKDGKVQATNSFSGVNYWLVKNKIEVFYPGPGHTPDNVVVWLPERKILFGGCFIKPYGLGNLGDANIEAWPKSAKLLKSKYGKAKLVVPSHSEVGDASLLKLTLEQAVKGLNESKKPSKPSN

Source Source

Source organism organism	Serratia marcescens
NCBI taxonomy ID ncbi_taxonomy_id	615
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	8

Entity 3 Entity 3 non-polymer

Description description	(2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid
Molecular weight formula_weight	279.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	492

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d6zysa_
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	d6zysb_
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	d6zysc_
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	d6zysd_
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	48.782 Å
Unit-cell length b length_b	77.969 Å
Unit-cell length c length_c	261.906 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	16

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	orthorhombic

Resolution resolution	1.870 Å
Low-resolution limit resolution_low	58.153 Å
R factor r_factor	0.1754
R_work r_work	0.1741
R_free r_free	0.2013

Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b

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

Beta-lactamase IMP-1

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

6zys__assembly_1__model_1

6zys__assembly_1__model_1 | I(q)

6zys__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 (4 domains)

7. Citations (1)

Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b

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

Beta-lactamase IMP-1

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

6zys__assembly_1__model_1

6zys__assembly_1__model_1 | I(q)

6zys__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 (4 domains)

7. Citations (1)