SAXSdb — 9mb4

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

Metallo-beta-lactamase type 2

Klebsiella pneumoniae

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 ;3,3-bis(oxidanyl)-9-[(4-thiophen-2-yl-1,2,3-triazol-1-yl)methyl]-2,5-dioxa-3-boranuidabicyclo[4.4.0]deca-1(6),7,9-triene-10-carboxylic acid ; × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ;3,3-bis(oxidanyl)-9-[(4-thiophen-2-yl-1,2,3-triazol-1-yl)methyl]-2,5-dioxa-3-boranuidabicyclo[4.4.0]deca-1(6),7,9-triene-10-carboxylic acid ; × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ;3,3-bis(oxidanyl)-9-[(4-thiophen-2-yl-1,2,3-triazol-1-yl)methyl]-2,5-dioxa-3-boranuidabicyclo[4.4.0]deca-1(6),7,9-triene-10-carboxylic acid ; × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	ZINC ION × 2 ;3,3-bis(oxidanyl)-9-[(4-thiophen-2-yl-1,2,3-triazol-1-yl)methyl]-2,5-dioxa-3-boranuidabicyclo[4.4.0]deca-1(6),7,9-triene-10-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	BLAN1_KLEPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–241； UniProt 30–270 Author chain B； PDBConstruct 1–241； UniProt 30–270 Author chain C； PDBConstruct 1–241； UniProt 30–270 Author chain D； PDBConstruct 1–241； UniProt 30–270

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	9mb4
Deposition date deposition_date	2025-03-15
Last revision last_revision	2026-03-11
Structure title title	Metal Beta Lactamase NDM-1 in Complex with Dual MBL/SBL Inhibitor 14
Keywords keywords	Beta Lactamase, Metallo Beta Lactamase NDM-1, Carbapenemase, 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.

9mb4__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9mb4__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9mb4__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	17.08 Å
Rg (electron density)	15.98 Å
Total Rg	16.93 Å
Atom count	3362
Residues	226
Excluded volume	30144 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9mb4__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9mb4__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`9mb4__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`9mb4__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 (4)

Entity 1 Entity 1 polymer

Description description	Metallo-beta-lactamase type 2
Molecular weight formula_weight	25574.8 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	13681

EIRPTIGQQMETGDQRFGDLVFRQLAPNVWQHTSYLDMPGFGAVASNGLIVRDGGRVLVVDTAWTDDQTAQILNWIKQEINLPVALAVVTHAHQDKMGGMDALHAAGIATYANALSNQLAPQEGMVAAQHSLTFAANGWVEPATAPNFGPLKVFYPGPGHTSDNITVGIDGTDIAFGGCLIKDSKAKSLGNLGDADTEHYAASARAFGAAFPKASMIVMSHSAPDSRAAITHTARMADKLR

Source Source

Source organism organism	Klebsiella pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	573
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	8

Entity 3 Entity 3 non-polymer

Description description	;3,3-bis(oxidanyl)-9-[(4-thiophen-2-yl-1,2,3-triazol-1-yl)methyl]-2,5-dioxa-3-boranuidabicyclo[4.4.0]deca-1(6),7,9-triene-10-carboxylic acid ;
Molecular weight formula_weight	374.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	231

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Unit-cell length a length_a	70.170 Å
Unit-cell length b length_b	73.601 Å
Unit-cell length c length_c	77.476 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.91 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.441 Å
Low-resolution limit resolution_low	42.498 Å
R factor r_factor	0.1792
R_work r_work	0.1726
R_free r_free	0.2713

Metal Beta Lactamase NDM-1 in Complex with Dual MBL/SBL Inhibitor 14

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

Metallo-beta-lactamase type 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

9mb4__assembly_3__model_1

9mb4__assembly_3__model_1 | I(q)

9mb4__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Metal Beta Lactamase NDM-1 in Complex with Dual MBL/SBL Inhibitor 14

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

Metallo-beta-lactamase type 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

9mb4__assembly_3__model_1

9mb4__assembly_3__model_1 | I(q)

9mb4__assembly_3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)