3l88

Crystal structure of the human Adenovirus type 21 fiber knob

Method: X-RAY DIFFRACTION D_max: 144.9 Å Quality: GOOD

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

Fiber protein

Human adenovirus 21

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 123–323 Chain B； UniProt 123–323 Chain C； UniProt 123–323	Fragment：Ad21 fiber knob (UNP residues 123-323)	NA SODIUM ION × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；298 K；22% PEG 3000, 0.2 M NaCl, 0.1 M Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.259
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 123–323 Chain E； UniProt 123–323 Chain F； UniProt 123–323	Fragment：Ad21 fiber knob (UNP residues 123-323)	NA SODIUM ION × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；298 K；22% PEG 3000, 0.2 M NaCl, 0.1 M Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.259
3	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 123–323 Chain H； UniProt 123–323 Chain I； UniProt 123–323	Fragment：Ad21 fiber knob (UNP residues 123-323)	NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；298 K；22% PEG 3000, 0.2 M NaCl, 0.1 M Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.259
4	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain J； UniProt 123–323 Chain K； UniProt 123–323 Chain L； UniProt 123–323	Fragment：Ad21 fiber knob (UNP residues 123-323)	NA SODIUM ION × 5 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.1；298 K；22% PEG 3000, 0.2 M NaCl, 0.1 M Tris, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.50 Å R-free 0.259

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3L88	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3L89 Human Adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP) Deposited 2009-12-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain B 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain C 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；6% PEG 8000, 0.1M LiCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.239
3L89 Human Adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP) Deposited 2009-12-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain E 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain F 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；6% PEG 8000, 0.1M LiCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.239
3L89 Human Adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP) Deposited 2009-12-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain H 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain I 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；6% PEG 8000, 0.1M LiCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.239
3L89 Human Adenovirus type 21 knob in complex with domains SCR1 and SCR2 of CD46 (membrane cofactor protein, MCP) Deposited 2009-12-30	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain J 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain K 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323) Chain L 123–323（201 aa） Fragment：Ad21 fiber knob (UNP residues 123-323)	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；6% PEG 8000, 0.1M LiCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.50 Å R-free 0.239

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q2KS96_9ADEN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–201； UniProt 123–323 Author chain B； PDBConstruct 1–201； UniProt 123–323 Author chain C； PDBConstruct 1–201； UniProt 123–323 Author chain D； PDBConstruct 1–201； UniProt 123–323 Author chain E； PDBConstruct 1–201； UniProt 123–323 Author chain F； PDBConstruct 1–201； UniProt 123–323 Author chain G； PDBConstruct 1–201； UniProt 123–323 Author chain H； PDBConstruct 1–201； UniProt 123–323 Author chain I； PDBConstruct 1–201； UniProt 123–323 Author chain J； PDBConstruct 1–201； UniProt 123–323 Author chain K； PDBConstruct 1–201； UniProt 123–323 Author chain L； PDBConstruct 1–201； UniProt 123–323

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3l88
Deposition date deposition_date	2009-12-30
Structure title title	Crystal structure of the human Adenovirus type 21 fiber knob
Keywords keywords	Adenovirus, Fiber Knob, Viral Protein; VIRAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	44.91 Å
Radius of gyration Rg (electron density) rg_electron	44.07 Å
Forward intensity I(0) i0	842494000.00
Molecular weight molecular_weight	242600.0 kDa
Excluded volume excluded_volume	304140 Å³
Envelope volume envelope_volume	412970 Å³
Hydration-shell volume shell_volume	75415 Å³
Envelope diameter envelope_diameter	145.0 Å
Shell Rg shell_rg	51.78 Å
Envelope Rg envelope_rg	42.86 Å
Shape Rg shape_rg	44.05 Å
Total Rg total_rg	44.46 Å
Total atoms total_atoms	17072
Residues n_residues	2195
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	144.9 Å
Rg (real space) rg_real	44.71 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	8.4250e+08
I(0) uncertainty (real space) i0_real_error	1.5250e+07
Rg (reciprocal space) rg_reciprocal	44.91 Å
I(0) (reciprocal space) i0_reciprocal	842700000.0000
Solution quality estimate total_estimate	0.8969
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	62.1 Å
Skewness Skewness skewness	0.108
Kurtosis Kurtosis kurtosis	-0.635
Angular range angular_range	— – 0.1750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	323700000.0000
Real-space data points n_real_points	36
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.908; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.933

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Fiber protein
Molecular weight formula_weight	22218.8 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	17174

GDICIKDSINTLWTGIKPPPNCQIVENTDTNDGKLTLVLVKNGGLVNGYVSLVGVSDTVNQMFTQKSATIQLRLYFDSSGNLLTDESNLKIPLKNKSSTATSEAATSSKAFMPSTTAYPFNTTTRDSENYIHGICYYMTSYDRSLVPLNISIMLNSRTISSNVAYAIQFEWNLNAKESPESNIATLTTSPFFFSYIREDDN

来源 Source

来源生物 organism	Human adenovirus 21
NCBI Class编号 ncbi_taxonomy_id	32608
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	11

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	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	67

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7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3l88a_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88b_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88c_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88d_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88e_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88f_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88g_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88h_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88i_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88j_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88k_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

Domain ID domain_id	d3l88l_
Class class	b — All beta proteins
Fold Fold fold	b.21 — Virus attachment protein globular domain
Superfamily Superfamily superfamily	b.21.1 — Virus attachment protein globular domain
Family Family family	b.21.1.0 — automated matches

CATH v4.4 (12 domains)

Domain ID domain_id	3l88A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88J00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

Domain ID domain_id	3l88L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	90 — Adenovirus Type 5 Fiber Protein (Receptor Binding Domain)
Homologous superfamily homologous superfamily	10 — Adenovirus pIV-related, attachment domain

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8. Citations (1)

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Unit-cell length a length_a	85.000 Å
Unit-cell length b length_b	63.920 Å
Unit-cell length c length_c	209.350 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.70 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 1 2 1
Space-group number int_tables_number	3
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	49.450 Å
R factor r_factor	0.2354
R_work r_work	0.2342
R_free r_free	0.2591

fit	/app/data/saxs_computation/l8/3l88/3l88.fit
pddf	/app/data/pr_computation/l8/3l88/3l88.pr.out
profile	/app/data/saxs_computation/l8/3l88/3l88.dat