2zc3

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae

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 homooligomer	Homooligomer	Protein 3	;(4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate ; × 1 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	;(4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate ; × 1 SULFATE ION × 1 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	;(4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate ; × 2 SULFATE ION × 1 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PBPX_STRR6
Isoform	—
PDB entities	1, 2, 3
Chains and sequence ranges	Author chain A； PDBConstruct 1–168； UniProt 71–238 Author chain D； PDBConstruct 1–168； UniProt 71–238 Author chain B； PDBConstruct 1–385； UniProt 241–625 Author chain E； PDBConstruct 1–385； UniProt 241–625 Author chain C； PDBConstruct 1–125； UniProt 626–750 Author chain F； PDBConstruct 1–125； UniProt 626–750

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	2zc3
Deposition date deposition_date	2007-11-02
Structure title title	Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae
Keywords keywords	;PEPTIDOGLYCAN SYNTHESIS, CELL WALL, PENICILLIN-BINDING, ANTIBIOTICS, BIAPENEM, Antibiotic resistance, Cell cycle, Cell division, Cell shape, Cell wall biogenesis/degradation, Membrane, Secreted, Transmembrane, BIOSYNTHETIC PROTEIN ;; BIOSYNTHETIC 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.

2zc3__assembly_1__model_1

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

Download this curve (.dat)

2zc3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zc3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	29.50 Å
Rg (electron density)	29.22 Å
Total Rg	29.79 Å
Atom count	5011
Residues	649
Excluded volume	88882 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zc3__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zc3__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zc3__assembly_3__model_1`	hexameric （6）	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	Penicillin-binding protein 2X
Molecular weight formula_weight	18473.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	10016

TVPAKRGTIYDRNGVPIAEDATSYNVYAVIDENYKSATGKILYVEKTQFNKVAEVFHKYLDMEESYVREQLSQPNLKQVSFGAKGNGITYANMMSIKKELEAAEVKGIDFTTSPNRSYPNGQFASSFIGLAQLHENEDGSKSLLGTSGMESSLNSILAGTDGIITYEK

Source Source

Source organism organism	Streptococcus pneumoniae
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Penicillin-binding protein 2X
Molecular weight formula_weight	42000.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

LGNIVPGTEQVSQRTMDGKDVYTTISSPLQSFMETQMDAFQEKVKGKYMTATLVSAKTGEILATTQRPTFDADTKEGITEDFVWRDILYQSNYEPGSTMKVMMLAAAIDNNTFPGGEVFNSSELKIADATIRDWDVNEGLTGGRMMTFSQGFAHSSNVGMTLLEQKMGDATWLDYLNRFKFGVPTRFGLTDEYAGQLPADNIVNIAQSSFGQGISVTQTQMIRAFTAIANDGVMLEPKFISAIYDPNDQTARKSQKEIVGNPVSKDAASLTRTNMVLVGTDPVYGTMYNHSTGKPTVTVPGQNVALKSGTAQIADEKNGGYLVGLTDYIFSAVSMSPAENPDFILYVTVQQPEHYSGIQLGEFANPILERASAMKDSLNLQTTAK

Source Source

Source organism organism	Streptococcus pneumoniae
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Penicillin-binding protein 2X
Molecular weight formula_weight	13707.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

ALEQVSQQSPYPMPSVKDISPGDLAEELRRNLVQPIVVGTGTKIKNSSAEEGKNLAPNQQVLILSDKAEEVPDMYGWTKETAETLAKWLNIELEFQGSGSTVQKQDVRANTAIKDIKKITLTLGD

Source Source

Source organism organism	Streptococcus pneumoniae
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	;(4R,5S)-3-(6,7-dihydro-5H-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-ylsulfanyl)-5-[(1S,2R)-1-formyl-2-hydroxypropyl]-4-meth yl-4,5-dihydro-1H-pyrrole-2-carboxylate ;
Molecular weight formula_weight	352.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	82

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2zc3b_
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	d2zc3c1
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	d2zc3c2
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	d2zc3e_
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	d2zc3f1
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	d2zc3f2
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

CATH v4.4 (6 domains)

Domain ID domain_id	2zc3A01
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	2zc3A02
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	2zc3B00
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	2zc3D01
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	2zc3D02
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	2zc3E00
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	106.789 Å
Unit-cell length b length_b	171.909 Å
Unit-cell length c length_c	88.666 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.510 Å
R factor r_factor	0.2369
R_work r_work	0.2345
R_free r_free	0.2813

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae

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

2zc3__assembly_1__model_1

2zc3__assembly_1__model_1 | I(q)

2zc3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Penicillin-binding protein 2X (PBP 2X) acyl-enzyme complex (biapenem) from Streptococcus pneumoniae

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

2zc3__assembly_1__model_1

2zc3__assembly_1__model_1 | I(q)

2zc3__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)