5BYG - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF AAV2 OBD-AAVS1 COMPLEX 2:1

Authors :   F. N. Musayev, C. R. Escalante

Date :   10 Jun 15 (Deposition) - 23 Sep 15 (Release) - 25 Nov 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,E,F  (1x)
Biol. Unit 2: C,D,G,H  (1x)

Keywords :   Protein-Dna Complex, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. N. Musayev, F. Zarate-Perez, C. Bishop, J. W. Burgner, C. R. Escalante
Structural Insights Into The Assembly Of The Adeno-Associated Virus Type 2 Rep68 Protein On The Integration Site Aavs1.
J. Biol. Chem. V. 290 27487 2015
PubMed-ID: 26370092 | Reference-DOI: 10.1074/JBC.M115.669960

Molecule 1 - PROTEIN REP78
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)PLYSS
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 1-210
	Gene	:	REP78
	Organism Common	:	AAV-2
	Organism Scientific	:	ADENO-ASSOCIATED VIRUS 2
	Organism Taxid	:	648242
	Strain	:	ISOLATE SRIVASTAVA/1982

*Molecule 2 - DNA (5'- D(CPTPCPGPGPCPGPCPTPCPGPCPTPCPGPCPTPCPGPCPT)- 3')**
	Chains	:	E, G
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

*Molecule 3 - DNA (5'- D(GPAPGPCPGPAPGPCPGPAPGPCPGPAPGPCPGPCPCPGPA)- 3')**
	Chains	:	F, H
	Engineered	:	YES
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synthetic	:	YES

		1	2	3	4	5	6	7	8
Asymmetric Unit	:	A	B	C	D	E	F	G	H
Biological Unit 1 (1x)	:	A	B			E	F
Biological Unit 2 (1x)	:			C	D			G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CIT	2	Ligand/Ion	CITRIC ACID
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:92	binding site for residue MG A 301
2	AC2	SOFTWARE	GLU A:150 , GLN A:174 , TYR A:175 , LEU A:188 , GLN A:191 , HIS A:192 , HIS A:195	binding site for residue CIT A 302
3	AC3	SOFTWARE	GLU B:83 , HIS B:90 , HIS B:92 , HOH B:406	binding site for residue MG B 301
4	AC4	SOFTWARE	GLU C:83 , HIS C:92 , LYS C:160	binding site for residue MG C 301
5	AC5	SOFTWARE	GLU C:150 , PRO C:154 , TYR C:175 , LEU C:188 , GLN C:191 , HIS C:192 , HIS C:195	binding site for residue CIT C 302

(no "SS Bond" information available for 5BYG)

Asymmetric Unit

No.	Residues
1	Gln A:162	-	Pro A:163
2	Gln B:162	-	Pro B:163
3	Gln C:162	-	Pro C:163
4	Gln D:162	-	Pro D:163

(no "SAP(SNP)/Variant" information available for 5BYG)

(no "PROSITE Motif" information available for 5BYG)

(no "Exon" information available for 5BYG)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee............hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee................hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5byg A   1 MPGFYEIVIKVPSEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQE 201
                                    10  ||    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200 
                                       13|                                                                                                                                                                       
                                        34

Chain B from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..........................hhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee................hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5byg B   1 MPGFYEIVIKVPSDGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQ 207
                                    10   ||   26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206 
                                        14|                                                                                                                                                                                          
                                         21

Chain C from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee.........hhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh...........eee................hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5byg C   1 MPGFYEIVIKVPSGISDSFVNWVAEKEWELPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQ 200
                                    10  ||    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197   
                                       13|                                                                                                                                                                                   
                                        21

Chain D from PDB  Type:PROTEIN  Length:180
                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhhhh............ee............ee..hhhhhhh.......eeeeee.hhhhh....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5byg D   1 MPGFYEIVIKPPDSDMDLNLIEQAPLTVAEKLQRDFLTEWRRVSKAPEALFFVQFEKGESYFHMHVLVETTGVKSMVLGRFLSQIREKLIQRIYRGIEPTLPNWFAVTKTRNGAGGGNKVVDESYIPNFLLPKTQPELQWAWTNMEQYLSACLNLTERKRLVAQHLTHVSQTQEQNKENQ 207
                                    10|       47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                    10|                                                                                                                                                                         
                                     38

Chain E from PDB  Type:DNA  Length:21
                                                     
                 5byg E   1 CTCGGCGCTCGCTCGCTCGCT  21
                                    10        20

Chain F from PDB  Type:DNA  Length:21
                                                     
                 5byg F  22 GAGCGAGCGAGCGAGCGCCGA  42
                                    31        41

Chain G from PDB  Type:DNA  Length:21
                                                     
                 5byg G   1 CTCGGCGCTCGCTCGCTCGCT  21
                                    10        20

Chain H from PDB  Type:DNA  Length:21
                                                     
                 5byg H  22 GAGCGAGCGAGCGAGCGCCGA  42
                                    31        41

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 5BYG)

(no "CATH Domain" information available for 5BYG)

(no "Pfam Domain" information available for 5BYG)

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Asymmetric Unit
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	Cis Peptide Bonds
		Gln A:162 - Pro A:163	[ RasMol ]
		Gln B:162 - Pro B:163	[ RasMol ]
		Gln C:162 - Pro C:163	[ RasMol ]
		Gln D:162 - Pro D:163	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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