1w8x

Structural analysis of PRD1

Method: X-RAY DIFFRACTION D_max: 215.9 Å Quality: GOOD

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

MAJOR CAPSID PROTEIN (PROTEIN P3)

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 × 900 PDB declaration: 900-MERIC（900） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395 Chain C； UniProt 1–395 Chain D； UniProt 1–395 Chain E； UniProt 1–395 Chain F； UniProt 1–395 Chain G； UniProt 1–395 Chain H； UniProt 1–395 Chain I； UniProt 1–395 Chain J； UniProt 1–395 Chain K； UniProt 1–395 Chain L； UniProt 1–395	Not recorded	PROTEIN P30 × 60 （P27391） PROTEIN P31 × 60 （P27384） PROTEIN P16 × 60 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
2	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395 Chain C； UniProt 1–395 Chain D； UniProt 1–395 Chain E； UniProt 1–395 Chain F； UniProt 1–395 Chain G； UniProt 1–395 Chain H； UniProt 1–395 Chain I； UniProt 1–395 Chain J； UniProt 1–395 Chain K； UniProt 1–395 Chain L； UniProt 1–395	Not recorded	PROTEIN P30 × 1 （P27391） PROTEIN P31 × 1 （P27384） PROTEIN P16 × 1 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
3	Protein heterocomplex Heteromer Protein × 75 PDB declaration: 75-meric（75） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395 Chain C； UniProt 1–395 Chain D； UniProt 1–395 Chain E； UniProt 1–395 Chain F； UniProt 1–395 Chain G； UniProt 1–395 Chain H； UniProt 1–395 Chain I； UniProt 1–395 Chain J； UniProt 1–395 Chain K； UniProt 1–395 Chain L； UniProt 1–395	Not recorded	PROTEIN P30 × 5 （P27391） PROTEIN P31 × 5 （P27384） PROTEIN P16 × 5 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
4	Protein heterocomplex Heteromer Protein × 90 PDB declaration: 90-meric（90） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395 Chain C； UniProt 1–395 Chain D； UniProt 1–395 Chain E； UniProt 1–395 Chain F； UniProt 1–395 Chain G； UniProt 1–395 Chain H； UniProt 1–395 Chain I； UniProt 1–395 Chain J； UniProt 1–395 Chain K； UniProt 1–395 Chain L； UniProt 1–395	Not recorded	PROTEIN P30 × 6 （P27391） PROTEIN P31 × 6 （P27384） PROTEIN P16 × 6 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
5	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395 Chain C； UniProt 1–395 Chain D； UniProt 1–395 Chain E； UniProt 1–395 Chain F； UniProt 1–395 Chain G； UniProt 1–395 Chain H； UniProt 1–395 Chain I； UniProt 1–395 Chain J； UniProt 1–395 Chain K； UniProt 1–395 Chain L； UniProt 1–395	Not recorded	PROTEIN P30 × 1 （P27391） PROTEIN P31 × 1 （P27384） PROTEIN P16 × 1 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
6	Protein heterocomplex Heteromer Protein × 900 PDB declaration: 900-meric（900） Consistent with protein copy count	Chain A； UniProt 1–395 Chain B； UniProt 1–395 Chain C； UniProt 1–395 Chain D； UniProt 1–395 Chain E； UniProt 1–395 Chain F； UniProt 1–395 Chain G； UniProt 1–395 Chain H； UniProt 1–395 Chain I； UniProt 1–395 Chain J； UniProt 1–395 Chain K； UniProt 1–395 Chain L； UniProt 1–395	Not recorded	PROTEIN P30 × 60 （P27391） PROTEIN P31 × 60 （P27384） PROTEIN P16 × 60 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 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 1W8X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CJD THE BACTERIOPHAGE PRD1 COAT PROTEIN, P3, IS STRUCTURALLY SIMILAR TO HUMAN ADENOVIRUS HEXON Deposited 1999-04-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.2；35% (W/V) MPD, 0.2 M NACL, 0.1 M SODIUM ACETATE, PH 4.2	Resolution 1.85 Å R-free 0.205
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW7 QUASI-ATOMIC RESOLUTION MODEL OF BACTERIOPHAGE PRD1 CAPSID, OBTAINED BY COMBINED CRYO-EM AND X-RAY CRYSTALLOGRAPHY. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.50 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1GW8 quasi-atomic resolution model of bacteriophage PRD1 sus607 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2002-03-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer TRIS；pH 7.2；TRIS cryo-EM vitrification conditions Cryogen ETHANE；ETHANE	Resolution 13.30 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 540 PDB declaration: 540-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 45 PDB declaration: 45-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 54 PDB declaration: 54-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB5 quasi-atomic resolution model of bacteriophage PRD1 P3-shell, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 9 PDB declaration: nonameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 12.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB7 quasi-atomic resolution model of bacteriophage PRD1 sus1 mutant, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 14.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 720 PDB declaration: 720-MERIC	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 60 PDB declaration: 60-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 72 PDB declaration: 72-meric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HB9 quasi-atomic resolution model of bacteriophage PRD1 wild type virion, obtained by combined cryo-EM and X-ray crystallography. Deposited 2001-04-13	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 12 PDB declaration: dodecameric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa） Chain D 1–394（394 aa） Chain E 1–394（394 aa） Chain F 1–394（394 aa） Chain G 1–394（394 aa） Chain H 1–394（394 aa） Chain I 1–394（394 aa） Chain J 1–394（394 aa） Chain K 1–394（394 aa） Chain L 1–394（394 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；PLUNGE VITRIFICATION	Resolution 25.00 Å
1HQN THE SELENOMETHIONINE DERIVATIVE OF P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1. Deposited 2000-12-18	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；30% MPD, 0.2 M NACL, 0.1 M SODIUM ACETATE, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.20 Å R-free 0.227
1HX6 P3, THE MAJOR COAT PROTEIN OF THE LIPID-CONTAINING BACTERIOPHAGE PRD1. Deposited 2001-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–394（394 aa） Chain B 1–394（394 aa） Chain C 1–394（394 aa）	Not recorded	CL CHLORIDE ION × 2 NA SODIUM ION × 7 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.2；298 K；30% MPD, 0.1 M sodium acetate, 0.2 M NaCl, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.65 Å R-free 0.208
7OOK Bacteriophage PRD1 Major Capsid Protein P3 in complex with CPZ Deposited 2021-05-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain B 1–395（395 aa） Chain C 1–395（395 aa）	Not recorded	NA SODIUM ION × 5 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 10 Z80 3-(2-chloro-10H-phenothiazin-10-yl)-N,N-dimethylpropan-1-amine × 3 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；please see: PMID: 10499799	Resolution 2.23 Å R-free 0.216

9 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COA3_BPPRD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 1–395； UniProt 1–395 Author chain C； PDBConstruct 1–395； UniProt 1–395 Author chain D； PDBConstruct 1–395； UniProt 1–395 Author chain E； PDBConstruct 1–395； UniProt 1–395 Author chain F； PDBConstruct 1–395； UniProt 1–395 Author chain G； PDBConstruct 1–395； UniProt 1–395 Author chain H； PDBConstruct 1–395； UniProt 1–395 Author chain I； PDBConstruct 1–395； UniProt 1–395 Author chain J； PDBConstruct 1–395； UniProt 1–395 Author chain K； PDBConstruct 1–395； UniProt 1–395 Author chain L； PDBConstruct 1–395； UniProt 1–395

PROTEIN P30

OrganismNot specified

UniProt P27391

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 × 900 PDB declaration: 900-MERIC（900） Consistent with protein copy count	Chain M； UniProt 1–83	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 720 （P22535） PROTEIN P31 × 60 （P27384） PROTEIN P16 × 60 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
2	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain M； UniProt 1–83	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 12 （P22535） PROTEIN P31 × 1 （P27384） PROTEIN P16 × 1 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
3	Protein heterocomplex Heteromer Protein × 75 PDB declaration: 75-meric（75） Consistent with protein copy count	Chain M； UniProt 1–83	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 60 （P22535） PROTEIN P31 × 5 （P27384） PROTEIN P16 × 5 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
4	Protein heterocomplex Heteromer Protein × 90 PDB declaration: 90-meric（90） Consistent with protein copy count	Chain M； UniProt 1–83	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 72 （P22535） PROTEIN P31 × 6 （P27384） PROTEIN P16 × 6 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
5	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain M； UniProt 1–83	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 12 （P22535） PROTEIN P31 × 1 （P27384） PROTEIN P16 × 1 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
6	Protein heterocomplex Heteromer Protein × 900 PDB declaration: 900-meric（900） Consistent with protein copy count	Chain M； UniProt 1–83	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 720 （P22535） PROTEIN P31 × 60 （P27384） PROTEIN P16 × 60 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	VPP_BPPRD
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain M； PDBConstruct 1–83； UniProt 1–83

PROTEIN P31

OrganismNot specified

UniProt P27384

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 × 900 PDB declaration: 900-MERIC（900） Consistent with protein copy count	Chain N； UniProt 1–126	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 720 （P22535） PROTEIN P30 × 60 （P27391） PROTEIN P16 × 60 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
2	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain N； UniProt 1–126	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 12 （P22535） PROTEIN P30 × 1 （P27391） PROTEIN P16 × 1 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
3	Protein heterocomplex Heteromer Protein × 75 PDB declaration: 75-meric（75） Consistent with protein copy count	Chain N； UniProt 1–126	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 60 （P22535） PROTEIN P30 × 5 （P27391） PROTEIN P16 × 5 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
4	Protein heterocomplex Heteromer Protein × 90 PDB declaration: 90-meric（90） Consistent with protein copy count	Chain N； UniProt 1–126	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 72 （P22535） PROTEIN P30 × 6 （P27391） PROTEIN P16 × 6 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
5	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain N； UniProt 1–126	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 12 （P22535） PROTEIN P30 × 1 （P27391） PROTEIN P16 × 1 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
6	Protein heterocomplex Heteromer Protein × 900 PDB declaration: 900-meric（900） Consistent with protein copy count	Chain N； UniProt 1–126	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 720 （P22535） PROTEIN P30 × 60 （P27391） PROTEIN P16 × 60 （P27392）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	VPC_BPPRD
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain N； PDBConstruct 1–126； UniProt 1–126

PROTEIN P16

OrganismNot specified

UniProt P27392

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 × 900 PDB declaration: 900-MERIC（900） Consistent with protein copy count	Chain P； UniProt 1–117	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 720 （P22535） PROTEIN P30 × 60 （P27391） PROTEIN P31 × 60 （P27384）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
2	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain P； UniProt 1–117	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 12 （P22535） PROTEIN P30 × 1 （P27391） PROTEIN P31 × 1 （P27384）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
3	Protein heterocomplex Heteromer Protein × 75 PDB declaration: 75-meric（75） Consistent with protein copy count	Chain P； UniProt 1–117	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 60 （P22535） PROTEIN P30 × 5 （P27391） PROTEIN P31 × 5 （P27384）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
4	Protein heterocomplex Heteromer Protein × 90 PDB declaration: 90-meric（90） Consistent with protein copy count	Chain P； UniProt 1–117	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 72 （P22535） PROTEIN P30 × 6 （P27391） PROTEIN P31 × 6 （P27384）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
5	Protein heterocomplex Heteromer Protein × 15 PDB declaration: pentadecameric（15） Consistent with protein copy count	Chain P； UniProt 1–117	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 12 （P22535） PROTEIN P30 × 1 （P27391） PROTEIN P31 × 1 （P27384）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å
6	Protein heterocomplex Heteromer Protein × 900 PDB declaration: 900-meric（900） Consistent with protein copy count	Chain P； UniProt 1–117	Not recorded	MAJOR CAPSID PROTEIN (PROTEIN P3) × 720 （P22535） PROTEIN P30 × 60 （P27391） PROTEIN P31 × 60 （P27384）	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.2；3.7 W/V PEG 8000, 400 MM NACL 100 MM POTASSIUM PHOSPHATE BUFFER PH 7.2	Resolution 4.20 Å

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	VPS_BPPRD
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–117； UniProt 1–117

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1w8x
Deposition date deposition_date	2004-10-01
Structure title title	Structural analysis of PRD1
Keywords keywords	VIRUS, P3 MAJOR CAPSID PROTEIN, P30 TAPE MEASURE, P31 PENTON PROTEIN, P16 MEMBRANE PROTEIN, VIRUS/VIRAL PROTEIN, ICOSAHEDRAL 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	61.52 Å
Radius of gyration Rg (electron density) rg_electron	61.57 Å
Forward intensity I(0) i0	4082980000.00
Molecular weight molecular_weight	539360.0 kDa
Excluded volume excluded_volume	674340 Å³
Envelope volume envelope_volume	977830 Å³
Hydration-shell volume shell_volume	130290 Å³
Envelope diameter envelope_diameter	232.0 Å
Shell Rg shell_rg	63.39 Å
Envelope Rg envelope_rg	61.90 Å
Shape Rg shape_rg	61.56 Å
Total Rg total_rg	61.62 Å
Total atoms total_atoms	38116
Residues n_residues	4904
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	215.9 Å
Rg (real space) rg_real	61.77 Å
Rg uncertainty (real space) rg_real_error	2.41 Å
I(0) (real space) i0_real	4.0830e+09
I(0) uncertainty (real space) i0_real_error	8.3920e+07
Rg (reciprocal space) rg_reciprocal	61.29 Å
I(0) (reciprocal space) i0_reciprocal	4080000000.0000
Solution quality estimate total_estimate	0.7940
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	66.4 Å
Skewness Skewness skewness	0.471
Kurtosis Kurtosis kurtosis	-0.128
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1152000000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	MAJOR CAPSID PROTEIN (PROTEIN P3)
Molecular weight formula_weight	43477.4 kDa
Source method src_method	nat
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	38116

MAQVQQLTPAQQAALRNQQAMAANLQARQIVLQQSYPVIQQVETQTFDPANRSVFDVTPANVGIVKGFLVKVTAAITNNHATEAVALTDFGPANLVQRVIYYDPDNQRHTETSGWHLHFVNTAKQGAPFLSSMVTDSPIKYGDVMNVIDAPATIAAGATGELTMYYWVPLAYSETDLTGAVLANVPQSKQRLKLEFANNNTAFAAVGANPLEAIYQGAGAADCEFEEISYTVYQSYLDQLPVGQNGYILPLIDLSTLYNLENSAQAGLTPNVDFVVQYANLYRYLSTIAVFDNGGSFNAGTDINYLSQRTANFSDTRKLDPKTWAAQTRRRIATDFPKGVYYCDNRDKPIYTLQYGNVGFVVNPKTVNQNARLLMGYEYFTSRTELVNAGTISTT

Entity 2 Entity 2 polymer

Description description	PROTEIN P30
Molecular weight formula_weight	9061.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

ALINPQFPYAGPVPIPGPAPTETMPLLNYRVEGRIAGIQQARQFMPFLQGPHRAVAEQTYHAIGTGIQMGQTFNQPLINTQEG

Entity 3 Entity 3 polymer

Description description	PROTEIN P31
Molecular weight formula_weight	13757.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	N

MNVNNPNQMTVTPVYNGCDSGEGPQSVRGYFDAVAGENVKYDLTYLADTQGFTGVQCIYIDNAENDGAFEIDVEETGQRIKCPAGKQGYFPLLVPGRAKFVARHLGSGKKSVPLFFLNFTIAQGVW

Entity 4 Entity 4 polymer

Description description	PROTEIN P16
Molecular weight formula_weight	12559.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MDKKKLLYWVGGGLVLILIWLWFRNRPAAQVASNWEGPPYMTYNQPQAGSVTLPVAGYTSPSPTLPNRNRSCGCNPAVSAAMAQGADLASKLTDSITSQLNDYASSLNDYLASQAGV

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (15 domains)

Domain ID domain_id	d1w8xa_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xb_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xc_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xd_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xe_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xf_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xg_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xh_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xi_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xj_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xk_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xl_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xm_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xn_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

Domain ID domain_id	d1w8xp_
Class class	i — Low resolution protein structures
Fold Fold fold	i.6 — Viruses and virus-receptor complexes
Superfamily Superfamily superfamily	i.6.1 — Viruses and virus-receptor complexes
Family Family family	i.6.1.1 — Viruses and virus-receptor complexes

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8. Citations (1)

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Unit-cell length a length_a	903.000 Å
Unit-cell length b length_b	920.600 Å
Unit-cell length c length_c	926.200 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	2880

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	4.200 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/w8/1w8x/1w8x.fit
pddf	/app/data/pr_computation/w8/1w8x/1w8x.pr.out
profile	/app/data/saxs_computation/w8/1w8x/1w8x.dat

Structural analysis of PRD1

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

MAJOR CAPSID PROTEIN (PROTEIN P3)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN P30

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN P31

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN P16

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 (4)

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

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (15 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)