SAXSdb — 5n89

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

Streptavidin

Streptomyces avidinii

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 8	GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2 × 4 GLYCEROL × 4 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 8	GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2 × 4 GLYCEROL × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SAV_STRAV
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–183； UniProt 1–183 Author chain B； PDBConstruct 1–183； UniProt 1–183 Author chain D； PDBConstruct 1–183； UniProt 1–183 Author chain F； PDBConstruct 1–183； UniProt 1–183 Author chain H； PDBConstruct 1–183； UniProt 1–183 Author chain K； PDBConstruct 1–183； UniProt 1–183 Author chain M； PDBConstruct 1–183； UniProt 1–183 Author chain O； PDBConstruct 1–183； UniProt 1–183

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	5n89
Deposition date deposition_date	2017-02-23
Structure title title	CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE GNSFDDWLASKG
Keywords keywords	biotin binding protein, STREPTAVIDIN, HPQ MOTIF, STREPTAVIDIN PEPTIDE 11101 COMPLEX; biotin 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.

5n89__assembly_1__model_1

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

Download this curve (.dat)

5n89__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5n89__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.42 Å
Rg (electron density)	22.15 Å
Total Rg	23.14 Å
Atom count	4033
Residues	535
Excluded volume	70108 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5n89__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5n89__assembly_2__model_1`	octameric （8）	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 (4)

Entity 1 Entity 1 polymer

Description description	Streptavidin
Molecular weight formula_weight	18849.7 kDa
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,F,H,K,M,O
Atom count atom_count	9309

MRKIVVAAIAVSLTTVSITASASADPSKDSKAQVSAAEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAASIDAAKKAGVNNGNPLDAVQQ

Source Source

Source organism organism	Streptomyces avidinii
NCBI taxonomy ID ncbi_taxonomy_id	1895
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	GLY-ASN-SER-PHE-ASP-ASP-TRP-LEU-ALA-SER-LYS-GLY-NH2
Molecular weight formula_weight	1295.4 kDa
Source method src_method	syn
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,E,G,I,J,L,N,P

GNSFDDWLASKGX

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1108

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6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id	5n89A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89B00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89D00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89F00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89H00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89K00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89M00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	5n89O00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

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Unit-cell length a length_a	58.310 Å
Unit-cell length b length_b	58.305 Å
Unit-cell length c length_c	88.285 Å
Unit-cell angle α angle_alpha	104.38 °
Unit-cell angle β angle_beta	91.03 °
Unit-cell angle γ angle_gamma	88.43 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.270 Å
Low-resolution limit resolution_low	85.510 Å
R factor r_factor	0.1814
R_work r_work	0.1802
R_free r_free	0.2037

CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE GNSFDDWLASKG

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

Streptavidin

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

5n89__assembly_1__model_1

5n89__assembly_1__model_1 | I(q)

5n89__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF STREPTAVIDIN WITH PEPTIDE GNSFDDWLASKG

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

Streptavidin

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

5n89__assembly_1__model_1

5n89__assembly_1__model_1 | I(q)

5n89__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

7. Citations (1)