1rp5

PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics

Method: X-RAY DIFFRACTION

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

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	SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PBPX_STRPN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–702； UniProt 1–702 Author chain B； PDBConstruct 1–702； UniProt 1–702

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	1rp5
Deposition date deposition_date	2003-12-03
Structure title title	PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics
Keywords keywords	PENICILLIN-BINDING PROTEIN, TRANSPEPTIDASE, ANTIBIOTIC RESISTANCE, PEPTIDOGLYCAN SYNTHESIS, CELL WALL, TRANSMEMBRANE; TRANSPEPTIDASE
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.

1rp5__assembly_1__model_1

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

Download this curve (.dat)

1rp5__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1rp5__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.50 Å
Rg (electron density)	30.32 Å
Total Rg	30.69 Å
Atom count	5133
Residues	687
Excluded volume	90685 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1rp5__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1rp5__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	penicillin-binding protein 2x
Molecular weight formula_weight	76906.0 kDa
EC 编号 ec_number	3.4.-.-
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	10315

GTGTRFGTDLAKEAKKVHQTTRTVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELETAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEKDRLGNIVPGTEQVSQQTVDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAMSAFGQGISVTQTQMLRAFTAIANDGVMLEPKFISALYDPNDQSVRKSQKEIVGNPVSKEAASVTRDHMVMVGTDPTYGTMYNHSTGKATVNVPGQNVALKSGTAEIADEKNGGYLTGSTNNIFSVVSMHPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKESLNLQTTAKALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETFAKWLNIELEFEGSGSTVQKQDVRANTAIKDIKKIKLTLGD

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	45

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1rp5a1
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	d1rp5a2
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	d1rp5a3
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	d1rp5a4
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	d1rp5b1
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	d1rp5b2
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	d1rp5b3
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	d1rp5b4
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	1rp5A01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	1rp5A02
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	1rp5A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2110 —

Domain ID domain_id	1rp5A04
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	1rp5B01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	70 —

Domain ID domain_id	1rp5B02
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	1rp5B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	2110 —

Domain ID domain_id	1rp5B04
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	194.989 Å
Unit-cell length b length_b	194.989 Å
Unit-cell length c length_c	154.245 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 42 2 2
Space-group number int_tables_number	93
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	42.000 Å
R factor r_factor	—
R_work r_work	0.2310
R_free r_free	0.2560

PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics

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

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

1rp5__assembly_1__model_1

1rp5__assembly_1__model_1 | I(q)

1rp5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (5)

PBP2x from Streptococcus pneumoniae strain 5259 with reduced susceptibility to beta-lactam antibiotics

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

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

1rp5__assembly_1__model_1

1rp5__assembly_1__model_1 | I(q)

1rp5__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (5)