2b87

Structural basis for molecular recognition in an affibody:affibody complex

Method: SOLUTION NMR

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

ZTaq affibody

Staphylococcus aureus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q70AB8_STAAU
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–58； UniProt 117–173 Author chain B； PDBConstruct 2–58； UniProt 117–173

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	2b87
Deposition date deposition_date	2005-10-06
Structure title title	Structural basis for molecular recognition in an affibody:affibody complex
Keywords keywords	PROTEIN-PROTEIN INTERACTIONS PROTEIN ENGINEERING, MOLECULAR RECOGNITION, NMR SPECTROSCOPY, INDUCED FIT, AFFIBODY, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	SOLUTION NMR

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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.

2b87__assembly_1__model_38

Assembly 1 · Model 38 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2b87__assembly_1__model_38 | I(q)

100 plotted points; both axes use logarithmic scales.

2b87__assembly_1__model_38 | P(r) · Pending

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

Rg（Guinier）	14.76 Å
Rg (electron density)	13.64 Å
Total Rg	14.86 Å
Atom count	1833
Residues	116
Excluded volume	16195 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2b87__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	2	`2b87__assembly_1__model_2`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	3	`2b87__assembly_1__model_3`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	4	`2b87__assembly_1__model_4`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	5	`2b87__assembly_1__model_5`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	6	`2b87__assembly_1__model_6`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	7	`2b87__assembly_1__model_7`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	8	`2b87__assembly_1__model_8`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	9	`2b87__assembly_1__model_9`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	10	`2b87__assembly_1__model_10`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	11	`2b87__assembly_1__model_11`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	12	`2b87__assembly_1__model_12`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	13	`2b87__assembly_1__model_13`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	14	`2b87__assembly_1__model_14`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	15	`2b87__assembly_1__model_15`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	16	`2b87__assembly_1__model_16`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	17	`2b87__assembly_1__model_17`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	18	`2b87__assembly_1__model_18`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	19	`2b87__assembly_1__model_19`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	20	`2b87__assembly_1__model_20`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	21	`2b87__assembly_1__model_21`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	22	`2b87__assembly_1__model_22`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	23	`2b87__assembly_1__model_23`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	24	`2b87__assembly_1__model_24`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	25	`2b87__assembly_1__model_25`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	26	`2b87__assembly_1__model_26`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	27	`2b87__assembly_1__model_27`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	28	`2b87__assembly_1__model_28`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	29	`2b87__assembly_1__model_29`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	30	`2b87__assembly_1__model_30`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	31	`2b87__assembly_1__model_31`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	32	`2b87__assembly_1__model_32`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	33	`2b87__assembly_1__model_33`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	34	`2b87__assembly_1__model_34`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	35	`2b87__assembly_1__model_35`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	36	`2b87__assembly_1__model_36`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	37	`2b87__assembly_1__model_37`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	38	`2b87__assembly_1__model_38`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	39	`2b87__assembly_1__model_39`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
1	40	`2b87__assembly_1__model_40`	dimeric （2）	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	ZTaq affibody
Molecular weight formula_weight	6491.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	73320

VDNKFNKELGWATWEIFNLPNLNGVQVKAFIDSLRDDPSQSANLLAEAKKLNDAQAPK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	anti-ZTaq affibody
Molecular weight formula_weight	6427.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

VDNKFNKERVIAIGEIMRLPNLNSLQVVAFINSLRDDPSQSANLLAEAKKLNDAQAPK

Source Source

Source organism organism	Staphylococcus aureus
NCBI taxonomy ID ncbi_taxonomy_id	1280
Host organism host_organism	Escherichia coli BL21(DE3)

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2b87a_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

Domain ID domain_id	d2b87b_
Class class	a — All alpha proteins
Fold Fold fold	a.8 — immunoglobulin/albumin-binding domain-like
Superfamily Superfamily superfamily	a.8.1 — Bacterial immunoglobulin/albumin-binding domains
Family Family family	a.8.1.1 — Immunoglobulin-binding protein A modules

CATH v4.4 (2 domains)

Domain ID domain_id	2b87A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

Domain ID domain_id	2b87B00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	420 — Immunoglobulin FC, subunit C

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Structural basis for molecular recognition in an affibody:affibody complex

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

ZTaq affibody

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

2b87__assembly_1__model_38

2b87__assembly_1__model_38 | I(q)

2b87__assembly_1__model_38 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)