2wad

PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)

Method: X-RAY DIFFRACTION

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

PENICILLIN-BINDING PROTEIN 2B

OrganismNot specified

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 × 3 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	ZINC ION × 3 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	ZINC ION × 3 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PBP2_STRR6
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–680； UniProt 1–680 Author chain B； PDBConstruct 1–680； UniProt 1–680 Author chain C； PDBConstruct 1–680； UniProt 1–680

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	2wad
Deposition date deposition_date	2009-02-05
Structure title title	PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)
Keywords keywords	;PEPTIDOGLYCAN SYNTHESIS, PENICILLIN-BINDING PROTEIN, TRANSMEMBRANE, ANTIBIOTIC RESISTANCE, CELL SHAPE, PEPTIDOGLYCAN, CELL MEMBRANE, CELL WALL BIOGENESIS/DEGRADATION, MEMBRANE, INFECTION, RESISTANCE, ANTIBIOTIC, PEPTIDE BINDING PROTEIN ;; PEPTIDE BINDING 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.

2wad__assembly_1__model_1

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

Download this curve (.dat)

2wad__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2wad__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.41 Å
Rg (electron density)	32.41 Å
Total Rg	32.84 Å
Atom count	4608
Residues	606
Excluded volume	81810 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2wad__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2wad__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2wad__assembly_3__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 2B
Molecular weight formula_weight	73815.5 kDa
EC 编号 ec_number	3.4.-.-
Source method src_method	nat
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	14408

MRKFNSHSIPIRLNLLFSIVILLFMTIIGRLLYMQVLNKDFYEKKLASASQTKVTTSSARGEIYDASGKPLVENTLKQVVSFTRSNKMTATDLKEIAKKLLTYVSISSPNLTERQLADYYLADPEIYKKTVEALPSEKRLDSDGNRLSESELYNNAVDSVPTSQLNYTEDEKKEIYLFSQLNAVGNFATGTIATDPLNDSQVAVIASISKEMPGISISTSWDRKILETSLSSIVGSVSSEKAGLPAEEAESYLKKGYSLNDRVGTSYLEKQYEEVLQGKRPVKEIHLDKHGDMESVENIEEGSKGKNIKLTIDLAFQDSVDALLKSYFNSELGNGGAKYSEGVYAVALNPQTGAVLSMSGLKHDLKTGELTPDSLGTVTNVFVPGSVVKAATISSGWENGVLSGNQTLTDQPIVFQGSAPIYSWYKLAYGSFPITAVEALEYSSNAYVVQTALGIMGQTYQPNMFVGTSNLESAMGKLRSTFGEYGLGSATGIDLPDESTGLVPKEYNFANFITNAFGQFDNYTPMQLAQYVATIANNGVRLAPHIVEGIYDNNDKGGLGELIQAIDTKEINKVNISESDMAILHQGFYQVSHGTSPLTTGRAFSDGATVSISGKTGTGESYVAGGQEATNTNAVAYAPTENPQIAVAVVFPHNTNLTKNVGPAIARDIINLYNQHHPMN

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	9

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	570

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	2wadA01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wadA02
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	2wadA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1230 — Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain

Domain ID domain_id	2wadA04
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	2wadB01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wadB02
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	2wadB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1230 — Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain

Domain ID domain_id	2wadB04
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	2wadC01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	70 — Ubiquitin Ligase Nedd4; Chain: W;
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2wadC02
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	2wadC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	1230 — Penicillin-binding protein, N-terminal non-catalytic domain, head sub-domain

Domain ID domain_id	2wadC04
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	128.788 Å
Unit-cell length b length_b	128.788 Å
Unit-cell length c length_c	123.139 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	9

Space group space_group	P 31
Space-group number int_tables_number	144
Crystal system crystal_system	—

Resolution resolution	2.180 Å
Low-resolution limit resolution_low	44.500 Å
R factor r_factor	0.2130
R_work r_work	0.2110
R_free r_free	0.2610

PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)

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

PENICILLIN-BINDING PROTEIN 2B

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

2wad__assembly_1__model_1

2wad__assembly_1__model_1 | I(q)

2wad__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)

PENICILLIN-BINDING PROTEIN 2B (PBP-2B) FROM STREPTOCOCCUS PNEUMONIAE (STRAIN 5204)

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

PENICILLIN-BINDING PROTEIN 2B

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

2wad__assembly_1__model_1

2wad__assembly_1__model_1 | I(q)

2wad__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (2)