1k25

PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate

Method: X-RAY DIFFRACTION

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

low-affinity PENICILLIN-BINDING PROTEIN 2X

Streptococcus pneumoniae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O34006_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–685； UniProt 66–750 Author chain B； PDBConstruct 1–685； UniProt 66–750 Author chain C； PDBConstruct 1–685； UniProt 66–750 Author chain D； PDBConstruct 1–685； UniProt 66–750

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	1k25
Deposition date deposition_date	2001-09-26
Structure title title	PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate
Keywords keywords	antibiotic resistance, clinical mutant, low-affinity penicillin-binding, MEMBRANE PROTEIN; MEMBRANE 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.

1k25__assembly_1__model_1

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

Download this curve (.dat)

1k25__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k25__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.60 Å
Rg (electron density)	24.73 Å
Total Rg	25.41 Å
Atom count	4161
Residues	556
Excluded volume	73610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k25__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k25__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1k25__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1k25__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 (2)

Entity 1 Entity 1 polymer

Description description	low-affinity PENICILLIN-BINDING PROTEIN 2X
Molecular weight formula_weight	75259.4 kDa
Mutation mutation	F364L
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	16786

HQITRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDKKYKSATGKILYVEDAQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGSKGNGITYANMMAIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRVGNIVPGTELVSQQTVDGKDVYTTLSSPLQSFMETQMDAFLEKVKGKYMTATLVSAKTGEILATTQRPTFNADTKEGITEDFVWRDILYQSNYEPGSAMKVMTLASSIDNNTFPSGEYFNSSELKIADATTRDWDVNEGLTTGGMMTFLQGFAHSSNVGMSLLEQKMGDATWLDYLKRFKFGVPTRFGLTDEYAGQLPADNIVSIAQSSFGQGISVTQTQMLRAFTAIANDGVMLEPKFISAIYDTNNQSVRKSQKEIVGNPVSKEAASTTRNHMILVGTDPLYGTMYNHYTGKPIITVPGQNVAVKSGTAQIADEKNGGYLVGSTNYIFSAVTMNPAENPDFILYVTVQQPEHYSGIQLGEFATPILERASAMKESLNLQSPAKNLDKVTTESSYAMPSIKDISPGELAEALRRNIVQPIVVGTGTKIKETSVEEGTNLAPNQQVLLLSDKVEEIPDMYGWKKETAETFAKWLDIELEFEGSGSVVQKQDVRTNTAIKNIKKIKLTLGD

Source Source

Source organism organism	Streptococcus pneumoniae
NCBI taxonomy ID ncbi_taxonomy_id	1313
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	21

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6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1k25a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25a3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.175 — Penicillin binding protein dimerisation domain
Superfamily Superfamily superfamily	d.175.1 — Penicillin binding protein dimerisation domain
Family Family family	d.175.1.1 — Penicillin binding protein dimerisation domain

Domain ID domain_id	d1k25a4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d1k25b1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25b2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25b3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.175 — Penicillin binding protein dimerisation domain
Superfamily Superfamily superfamily	d.175.1 — Penicillin binding protein dimerisation domain
Family Family family	d.175.1.1 — Penicillin binding protein dimerisation domain

Domain ID domain_id	d1k25b4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d1k25c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25c3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.175 — Penicillin binding protein dimerisation domain
Superfamily Superfamily superfamily	d.175.1 — Penicillin binding protein dimerisation domain
Family Family family	d.175.1.1 — Penicillin binding protein dimerisation domain

Domain ID domain_id	d1k25c4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

Domain ID domain_id	d1k25d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25d2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.11 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Superfamily Superfamily superfamily	d.11.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain
Family Family family	d.11.1.1 — Penicillin-binding protein 2x (pbp-2x), c-terminal domain

Domain ID domain_id	d1k25d3
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.175 — Penicillin binding protein dimerisation domain
Superfamily Superfamily superfamily	d.175.1 — Penicillin binding protein dimerisation domain
Family Family family	d.175.1.1 — Penicillin binding protein dimerisation domain

Domain ID domain_id	d1k25d4
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.3 — beta-lactamase/transpeptidase-like
Superfamily Superfamily superfamily	e.3.1 — beta-lactamase/transpeptidase-like
Family Family family	e.3.1.1 — beta-Lactamase/D-ala carboxypeptidase

CATH v4.4 (8 domains)

Domain ID domain_id	1k25A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 2a (Domain 2)

Domain ID domain_id	1k25A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	1k25B01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 2a (Domain 2)

Domain ID domain_id	1k25B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	1k25C01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 2a (Domain 2)

Domain ID domain_id	1k25C02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

Domain ID domain_id	1k25D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1310 — Penicillin-binding protein 2a (Domain 2)
Homologous superfamily homologous superfamily	10 — Penicillin-binding protein 2a (Domain 2)

Domain ID domain_id	1k25D02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	710 — Beta-lactamase
Homologous superfamily homologous superfamily	10 — DD-peptidase/beta-lactamase superfamily

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Unit-cell length a length_a	146.560 Å
Unit-cell length b length_b	146.560 Å
Unit-cell length c length_c	132.610 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	12

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	3.200 Å
Low-resolution limit resolution_low	19.900 Å
R factor r_factor	0.2350
R_work r_work	0.2350
R_free r_free	0.3120

PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate

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

low-affinity PENICILLIN-BINDING PROTEIN 2X

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

1k25__assembly_1__model_1

1k25__assembly_1__model_1 | I(q)

1k25__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)

PBP2x from a Highly Penicillin-resistant Streptococcus pneumoniae Clinical Isolate

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

low-affinity PENICILLIN-BINDING PROTEIN 2X

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

1k25__assembly_1__model_1

1k25__assembly_1__model_1 | I(q)

1k25__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (16 domains)

CATH v4.4 (8 domains)

7. Citations (1)