SAXSdb — 1cd3

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

PROTEIN (SCAFFOLDING PROTEIN GPD)

OrganismNot specified

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 heterocomplex Heteromer Protein × 420 PDB declaration: 420-MERIC（420） Consistent with protein copy count	Chain 1； UniProt 1–151 Chain 2； UniProt 1–151 Chain 3； UniProt 1–151 Chain 4； UniProt 1–151	Not recorded	PROTEIN (CAPSID PROTEIN GPF) × 60 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 60 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 60 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain 1； UniProt 1–151 Chain 2； UniProt 1–151 Chain 3； UniProt 1–151 Chain 4； UniProt 1–151	Not recorded	PROTEIN (CAPSID PROTEIN GPF) × 1 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 1 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
3	Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count	Chain 1； UniProt 1–151 Chain 2； UniProt 1–151 Chain 3； UniProt 1–151 Chain 4； UniProt 1–151	Not recorded	PROTEIN (CAPSID PROTEIN GPF) × 5 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 5 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 5 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
4	Protein heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain 1； UniProt 1–151 Chain 2； UniProt 1–151 Chain 3； UniProt 1–151 Chain 4； UniProt 1–151	Not recorded	PROTEIN (CAPSID PROTEIN GPF) × 6 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 6 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 6 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
5	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain 1； UniProt 1–151 Chain 2； UniProt 1–151 Chain 3； UniProt 1–151 Chain 4； UniProt 1–151	Not recorded	PROTEIN (CAPSID PROTEIN GPF) × 1 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 1 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
6	Protein heterocomplex Heteromer Protein × 280 PDB declaration: 280-meric（280） Consistent with protein copy count	Chain 1； UniProt 1–151 Chain 2； UniProt 1–151 Chain 3； UniProt 1–151 Chain 4； UniProt 1–151	Not recorded	PROTEIN (CAPSID PROTEIN GPF) × 40 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 40 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 40 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å

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 1CD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly	Chain 1 1–151（151 aa） Chain 2 1–151（151 aa） Chain 3 1–151（151 aa） Chain 4 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 1 1–151（151 aa） Chain 2 1–151（151 aa） Chain 3 1–151（151 aa） Chain 4 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain 1 1–151（151 aa） Chain 2 1–151（151 aa） Chain 3 1–151（151 aa） Chain 4 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain 1 1–151（151 aa） Chain 2 1–151（151 aa） Chain 3 1–151（151 aa） Chain 4 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain 1 1–151（151 aa） Chain 2 1–151（151 aa） Chain 3 1–151（151 aa） Chain 4 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric	Chain 1 1–151（151 aa） Chain 2 1–151（151 aa） Chain 3 1–151（151 aa） Chain 4 1–151（151 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å

1 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGD_BPPHX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain 1； PDBConstruct 1–152； UniProt 1–151 Author chain 2； PDBConstruct 1–152； UniProt 1–151 Author chain 3； PDBConstruct 1–152； UniProt 1–151 Author chain 4； PDBConstruct 1–152； UniProt 1–151

PROTEIN (CAPSID PROTEIN GPF)

OrganismNot specified

UniProt P03641

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 heterocomplex Heteromer Protein × 420 PDB declaration: 420-MERIC（420） Consistent with protein copy count	Chain F； UniProt 1–426	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 240 （P69486） PROTEIN (SPIKE PROTEIN GPG) × 60 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 60 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain F； UniProt 1–426	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 （P69486） PROTEIN (SPIKE PROTEIN GPG) × 1 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
3	Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count	Chain F； UniProt 1–426	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 20 （P69486） PROTEIN (SPIKE PROTEIN GPG) × 5 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 5 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
4	Protein heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain F； UniProt 1–426	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 24 （P69486） PROTEIN (SPIKE PROTEIN GPG) × 6 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 6 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
5	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain F； UniProt 1–426	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 （P69486） PROTEIN (SPIKE PROTEIN GPG) × 1 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
6	Protein heterocomplex Heteromer Protein × 280 PDB declaration: 280-meric（280） Consistent with protein copy count	Chain F； UniProt 1–426	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 160 （P69486） PROTEIN (SPIKE PROTEIN GPG) × 40 （P03643） PROTEIN (SCAFFOLDING PROTEIN GPB) × 40 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å

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 1CD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly	Chain F 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain F 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain F 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain F 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric	Chain F 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-MERIC	Chain A 1–426（426 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–426（426 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–426（426 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–426（426 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 27.00 Å
1KVP STRUCTURAL ANALYSIS OF THE SPIROPLASMA VIRUS, SPV4, IMPLICATIONS FOR EVOLUTIONARY VARIATION TO OBTAIN HOST DIVERSITY AMONG THE MICROVIRIDAE, ELECTRON MICROSCOPY, ALPHA CARBONS ONLY Deposited 1997-12-12	Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–426（426 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 9.2；50 mM Sodium tetraborate cryo-EM vitrification conditions Cryogen ETHANE	Resolution 27.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC	Chain 1 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain 1 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric	Chain 1 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric	Chain 1 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain 1 1–426（426 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å

3 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGF_BPPHX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain F； PDBConstruct 1–426； UniProt 1–426

PROTEIN (SPIKE PROTEIN GPG)

OrganismNot specified

UniProt P03643

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 heterocomplex Heteromer Protein × 420 PDB declaration: 420-MERIC（420） Consistent with protein copy count	Chain G； UniProt 1–175	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 240 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 60 （P03641） PROTEIN (SCAFFOLDING PROTEIN GPB) × 60 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain G； UniProt 1–175	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 1 （P03641） PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
3	Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count	Chain G； UniProt 1–175	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 20 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 5 （P03641） PROTEIN (SCAFFOLDING PROTEIN GPB) × 5 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
4	Protein heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain G； UniProt 1–175	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 24 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 6 （P03641） PROTEIN (SCAFFOLDING PROTEIN GPB) × 6 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
5	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain G； UniProt 1–175	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 1 （P03641） PROTEIN (SCAFFOLDING PROTEIN GPB) × 1 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
6	Protein heterocomplex Heteromer Protein × 280 PDB declaration: 280-meric（280） Consistent with protein copy count	Chain G； UniProt 1–175	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 160 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 40 （P03641） PROTEIN (SCAFFOLDING PROTEIN GPB) × 40 （P03633）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å

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 1CD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly	Chain G 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain G 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain G 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric	Chain G 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 180 PDB declaration: 240-MERIC	Chain 2 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain 2 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–DNA Heteromer；Protein × 15 PDB declaration: eicosameric	Chain 2 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric	Chain 2 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPA ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS Deposited 1991-12-03	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 5 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric	Chain 2 1–175（175 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å

2 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGG_BPPHX
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 1–175； UniProt 1–175

PROTEIN (SCAFFOLDING PROTEIN GPB)

OrganismNot specified

UniProt P03633

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 heterocomplex Heteromer Protein × 420 PDB declaration: 420-MERIC（420） Consistent with protein copy count	Chain B； UniProt 1–120	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 240 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 60 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 60 （P03643）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
2	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain B； UniProt 1–120	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 1 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 1 （P03643）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
3	Protein heterocomplex Heteromer Protein × 35 PDB declaration: 35-meric（35） Consistent with protein copy count	Chain B； UniProt 1–120	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 20 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 5 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 5 （P03643）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
4	Protein heterocomplex Heteromer Protein × 42 PDB declaration: 42-meric（42） Consistent with protein copy count	Chain B； UniProt 1–120	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 24 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 6 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 6 （P03643）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
5	Protein heterocomplex Heteromer Protein × 7 PDB declaration: heptameric（7） Consistent with protein copy count	Chain B； UniProt 1–120	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 4 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 1 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 1 （P03643）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å
6	Protein heterocomplex Heteromer Protein × 280 PDB declaration: 280-meric（280） Consistent with protein copy count	Chain B； UniProt 1–120	Not recorded	PROTEIN (SCAFFOLDING PROTEIN GPD) × 160 （P69486） PROTEIN (CAPSID PROTEIN GPF) × 40 （P03641） PROTEIN (SPIKE PROTEIN GPG) × 40 （P03643）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, VAPOR DIFFUSION	Resolution 3.50 Å

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 1CD3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 420 PDB declaration: complete icosahedral assembly	Chain B 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 2 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 3 Protein heterocomplex Heteromer；Protein × 35 PDB declaration: 35-meric	Chain B 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 4 Protein heterocomplex Heteromer；Protein × 42 PDB declaration: 42-meric	Chain B 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 5 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain B 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å
1AL0 PROCAPSID OF BACTERIOPHAGE PHIX174 Deposited 1997-06-06	Different experimental conditions	Assembly 6 Protein heterocomplex Heteromer；Protein × 280 PDB declaration: 280-meric	Chain B 1–120（120 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；PROCAPSIDS WERE CRYSTALLIZED BY VAPOUR DIFFUSION FROM 43-37% (OF SATURATION) AMMONIUM SULFATE, 100MM MES PH6.0, vapor diffusion	Resolution 3.50 Å

1 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGB_BPPHX
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain B； PDBConstruct 1–120； UniProt 1–120

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	1cd3
Deposition date deposition_date	1999-03-05
Structure title title	PROCAPSID OF BACTERIOPHAGE PHIX174
Keywords keywords	COMPLEX (VIRUS CAPSID PROTEINS), BACTERIOPHAGE, PROCAPSID, SCAFFOLDING PROTEIN, CHAPERONE, Icosahedral virus, Virus; VIRUS
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	35.98 Å
Radius of gyration Rg (electron density) rg_electron	35.09 Å
Forward intensity I(0) i0	292532000.00
Molecular weight molecular_weight	138320.0 kDa
Excluded volume excluded_volume	173230 Å³
Envelope volume envelope_volume	235970 Å³
Hydration-shell volume shell_volume	54525 Å³
Envelope diameter envelope_diameter	116.5 Å
Shell Rg shell_rg	42.59 Å
Envelope Rg envelope_rg	35.10 Å
Shape Rg shape_rg	35.06 Å
Total Rg total_rg	35.73 Å
Total atoms total_atoms	9755
Residues n_residues	1233
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	108.8 Å
Rg (real space) rg_real	35.76 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	2.9250e+08
I(0) uncertainty (real space) i0_real_error	4.1890e+06
Rg (reciprocal space) rg_reciprocal	35.90 Å
I(0) (reciprocal space) i0_reciprocal	292600000.0000
Solution quality estimate total_estimate	0.9060
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.0 Å
Skewness Skewness skewness	0.078
Kurtosis Kurtosis kurtosis	-0.570
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	46470000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.910

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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	PROTEIN (SCAFFOLDING PROTEIN GPD)
Molecular weight formula_weight	16953.3 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	1,2,3,4
Atom count atom_count	9851

MSQVTEQSVRFQTALASIKLIQASAVLDLTEDDFDFLTSNKVWIATDRSRARRCVEACVYGTLDFVGYPRFPAPVEFIAAVIAYYVHPVNIQTACLIMEGAEFTENIINGVERPVKAAELFAFTLRVRAGNTDVLTDAEENVRQKLRAEGVM

Entity 2 Entity 2 polymer

Description description	PROTEIN (CAPSID PROTEIN GPF)
Molecular weight formula_weight	48407.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

SNIQTGAERMPHDLSHLGFLAGQIGRLITISTTPVIAGDSFEMDAVGALRLSPLRRGLAIDSTVDIFTFYVPHRHVYGEQWIKFMKDGVNATPLPTVNTTGYIDHAAFLGTINPDTNKIPKHLFQGYLNIYNNYFKAPWMPDRTEANPNELNQDDARFGFRCCHLKNIWTAPLPPETELSRQMTTSTTSIDIMGLQAAYANLHTDQERDYFMQRYRDVISSFGGKTSYDADNRPLLVMRSNLWASGYDVDGTDQTSLGQFSGRVQQTYKHSVPRFFVPEHGTMFTLALVRFPPTATKEIQYLNAKGALTYTDIAGDPVLYGNLPPREISMKDVFRSGDSSKKFKIAEGQWYRYAPSYVSPAYHLLEGFPFIQEPPSGDLQERVLIRHHDYDQCFQSVQLLQWNSQVKFNVTVYRNLPTTRDSIMTS

Entity 3 Entity 3 polymer

Description description	PROTEIN (SPIKE PROTEIN GPG)
Molecular weight formula_weight	19061.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MFQTFISRHNSNFFSDKLVLTSVTPASSAPVLQTPKATSSTLYFDSLTVNAGNGGFLHCIQMDTSVNAANQVVSVGADIAFDADPKFFACLVRFESSSVPTTLPTAYDVYPLNGRHDGGYYTVKDCVTIDVLPRTPGNNVYVGFMVWSNFTATKCRGLVSLNQVIKEIICLQPLK

Entity 4 Entity 4 polymer

Description description	PROTEIN (SCAFFOLDING PROTEIN GPB)
Molecular weight formula_weight	13863.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MEQLTKNQAVATSQEAVQNQNEPQLRDENAHNDKSVHGVLNPTYQAGLRRDAVQPDIEAERKKRDEIEAGKSYCSRRFGGATCDDKSAQIYARFDKNDWRIQPAEFYRFHDAEVNTFGYF

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	96

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7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1cd31_
Class class	a — All alpha proteins
Fold Fold fold	a.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamily	a.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family family	a.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid

Domain ID domain_id	d1cd32_
Class class	a — All alpha proteins
Fold Fold fold	a.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamily	a.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family family	a.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid

Domain ID domain_id	d1cd33_
Class class	a — All alpha proteins
Fold Fold fold	a.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamily	a.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family family	a.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid

Domain ID domain_id	d1cd34_
Class class	a — All alpha proteins
Fold Fold fold	a.84 — Scaffolding protein gpD of bacteriophage procapsid
Superfamily Superfamily superfamily	a.84.1 — Scaffolding protein gpD of bacteriophage procapsid
Family Family family	a.84.1.1 — Scaffolding protein gpD of bacteriophage procapsid

Domain ID domain_id	d1cd3f_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.1 — Microviridae-like VP

Domain ID domain_id	d1cd3g_
Class class	b — All beta proteins
Fold Fold fold	b.121 — Nucleoplasmin-like/VP (viral coat and capsid proteins)
Superfamily Superfamily superfamily	b.121.5 — ssDNA viruses
Family Family family	b.121.5.1 — Microviridae-like VP

CATH v4.4 (7 domains)

Domain ID domain_id	1cd3100
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily	10 — Scaffold protein D

Domain ID domain_id	1cd3200
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily	10 — Scaffold protein D

Domain ID domain_id	1cd3300
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily	10 — Scaffold protein D

Domain ID domain_id	1cd3400
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1850 — Procapsid Of Bacteriophage Phix174, Chain 1
Homologous superfamily homologous superfamily	10 — Scaffold protein D

Domain ID domain_id	1cd3B00
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	1260 — Scaffolding protein gpD of bacteriophage procapsid fold
Homologous superfamily homologous superfamily	10 — Scaffolding protein gpD of bacteriophage procapsid

Domain ID domain_id	1cd3F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	169 — Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1
Homologous superfamily homologous superfamily	10 — Microviridae F protein

Domain ID domain_id	1cd3G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	20 —

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8. Citations (7)

The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174.

J.Mol.Biol. (1999)

PMID: 10329166 · DOI: 10.1006/jmbi.1999.2699 PRIMARY

Structure of a viral procapsid with molecular scaffolding.

Nature (1997)

PMID: 9305849 · DOI: 10.1038/38537

DNA packaging intermediates of bacteriophage phi X174.

Structure (1995)

PMID: 7613866 · DOI: 10.1016/s0969-2126(01)00167-8

Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A.

J.Mol.Biol. (1994)

PMID: 8158636 · DOI: 10.1006/jmbi.1994.1253

Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications.

Nature (1992)

PMID: 1370343 · DOI: 10.1038/355137a0

The Bacteriophages

The Bacteriophages (The Viruses) (1988)

Nucleotide sequence of bacteriophage phi X174 DNA.

Nature (1977)

PMID: 870828 · DOI: 10.1038/265687a0

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Unit-cell length a length_a	774.000 Å
Unit-cell length b length_b	774.000 Å
Unit-cell length c length_c	774.000 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	96

Space group space_group	I 21 3
Space-group number int_tables_number	199
Crystal system crystal_system	—

Resolution resolution	3.500 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2750
R_free r_free	—

fit	/app/data/saxs_computation/cd/1cd3/1cd3.fit
pddf	/app/data/pr_computation/cd/1cd3/1cd3.pr.out
profile	/app/data/saxs_computation/cd/1cd3/1cd3.dat

PROCAPSID OF BACTERIOPHAGE PHIX174

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

PROTEIN (SCAFFOLDING PROTEIN GPD)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (CAPSID PROTEIN GPF)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (SPIKE PROTEIN GPG)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (SCAFFOLDING PROTEIN GPB)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 13 domains

SCOP 2.08 (6 domains)

CATH v4.4 (7 domains)

8. Citations (7)

9. Files and Curves (10)

Files (7)

Curves (3)