5UOP - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE PROTOTYPE FOAMY VIRUS INTASOME WITH A 2-PYRIDINONE AMINAL INHIBITOR (COMPOUND 18)

Authors :   D. J. Klein

Date :   01 Feb 17 (Deposition) - 29 Mar 17 (Release) - 19 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Dna Integration, Viral Protein, Recombination-Inhibitor-Dna Complex, Transferase-Dna-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. D. Schreier, M. W. Embrey, I. T. Raheem, G. Barbe, L. C. Campeau, D. Dubost, J. Mccabe Dunn, J. Grobler, T. J. Hartingh, D. J. Hazuda, D. Klein, M. D. Miller, K. P. Moore, N. Nguyen, N. Pajkovic, D. A. Powell V. Rada, J. M. Sanders, J. Sisko, T. G. Steele, J. Wai, A. Walji, M. Xu, P. J. Coleman
Discovery And Optimization Of 2-Pyridinone Aminal Integrase Strand Transfer Inhibitors For The Treatment Of Hiv.
Bioorg. Med. Chem. Lett. V. 27 2038 2017
PubMed-ID: 28285916 | Reference-DOI: 10.1016/J.BMCL.2017.02.039

Molecule 1 - INTEGRASE
	Chains	:	A, B
	EC Number	:	2.7.7.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	POL
	Organism Common	:	SFVCPZ(HU)
	Organism Scientific	:	HUMAN SPUMARETROVIRUS
	Organism Taxid	:	11963
	Synonym	:	PR125POL

Molecule 2 - NUCLEOTIDE PREPROCESSED PFV DONOR DNA (NON-TRANSFERRED STRAND)
	Chains	:	C
	Engineered	:	YES
	Organism Scientific	:	HUMAN SPUMARETROVIRUS
	Organism Taxid	:	11963
	Synthetic	:	YES

Molecule 3 - NUCLEOTIDE PREPROCESSED PFV DONOR DNA (TRANSFERRED STRAND)
	Chains	:	D
	Engineered	:	YES
	Organism Scientific	:	HUMAN SPUMARETROVIRUS
	Organism Taxid	:	11963
	Synthetic	:	YES

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 13)

No.	Name	Count	Type	Full Name
1	8G4	1	Ligand/Ion	(1S,2S,5R)-8'-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-2'-[2-(2,5-DIOXO-2,5-DIHYDRO-1H-PYRROL-1-YL)ETHYL]-6'-HYDROXY-9',10'-DIHYDRO-2'H-SPIRO[BICYCLO[3.1.0]HEXANE-2,3'-IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE]-1',5',7'(8'H)-TRIONE
2	GOL	5	Ligand/Ion	GLYCEROL
3	MG	3	Ligand/Ion	MAGNESIUM ION
4	SO4	3	Ligand/Ion	SULFATE ION
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (3, 18)

No.	Name	Count	Type	Full Name
1	8G4	2	Ligand/Ion	(1S,2S,5R)-8'-[(3-CHLORO-4-FLUOROPHENYL)METHYL]-2'-[2-(2,5-DIOXO-2,5-DIHYDRO-1H-PYRROL-1-YL)ETHYL]-6'-HYDROXY-9',10'-DIHYDRO-2'H-SPIRO[BICYCLO[3.1.0]HEXANE-2,3'-IMIDAZO[5,1-A][2,6]NAPHTHYRIDINE]-1',5',7'(8'H)-TRIONE
2	GOL	10	Ligand/Ion	GLYCEROL
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	SO4	6	Ligand/Ion	SULFATE ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:62 , HIS A:66 , CYS A:96 , CYS A:99	binding site for residue ZN A 401
02	AC2	SOFTWARE	SER A:162 , THR A:163 , SER A:164 , HOH A:523	binding site for residue GOL A 402
03	AC3	SOFTWARE	PRO A:135 , SER A:136 , GLN A:137 , LYS A:241	binding site for residue GOL A 403
04	AC4	SOFTWARE	ASP A:128 , ASP A:185 , MG A:405 , GOL A:408 , 8G4 A:409 , HOH A:501 , HOH A:513	binding site for residue MG A 404
05	AC5	SOFTWARE	ASP A:128 , GLU A:221 , ASN A:224 , MG A:404 , 8G4 A:409 , HOH D:101	binding site for residue MG A 405
06	AC6	SOFTWARE	LYS A:228 , SER A:332 , LEU A:333 , ARG A:336 , HOH A:530 , HOH A:539 , DA D:17	binding site for residue SO4 A 406
07	AC7	SOFTWARE	HIS A:338 , LYS A:339 , HIS A:357 , HOH A:561	binding site for residue SO4 A 407
08	AC8	SOFTWARE	TYR A:129 , GLY A:131 , MG A:404 , 8G4 A:409 , HOH A:501	binding site for residue GOL A 408
09	AC9	SOFTWARE	ASP A:128 , ASP A:185 , GLY A:187 , PRO A:214 , GLN A:215 , GLU A:221 , MG A:404 , MG A:405 , GOL A:408 , DG C:4 , DC D:16 , DA D:17	binding site for residue 8G4 A 409
10	AD1	SOFTWARE	LYS B:219 , ARG B:222 , SER B:258 , PRO B:259 , VAL B:260	binding site for residue SO4 B 401
11	AD2	SOFTWARE	LEU A:292 , GLN A:296 , TYR B:263 , GLY B:271 , ASP B:273	binding site for residue GOL B 402
12	AD3	SOFTWARE	ASP B:128 , ASP B:185	binding site for residue MG B 403
13	AD4	SOFTWARE	TYR A:303 , DC C:6 , DA C:7 , DT C:8 , HOH C:205 , HOH C:207 , DC D:11 , HOH D:105	binding site for residue GOL C 101

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

Asymmetric Unit

No.	Residues
1	Gly A:131	-	Pro A:132
2	Gly B:131	-	Pro B:132

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

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

(no "Exon" information available for 5UOP)

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:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhh...........eeee..eeeeee..eeee..hhhhhhhhhhhhhh....hhhhhhhhhh......hhhhhhhhhhh.hhhhhhhh....ee..............eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhhhhh............ee......eeee...............eeeeeeee..eeeee.....eeeee...eee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uop A   8 LDAELDQLLQGHYIKGYPKQYTYFLEDGKVKVSRPEGVKIIPPQSDRQKIVLQAHNLAHTGREATLLKIANLYWWPNMRKDVVKQLGRCQQCLITNASNKASGPILRPDRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIRTSLYHPSTPPASSRSWSPVVGQLVQERVARPASLRPRWHKPSTVLKVLNPRTVVILDHLGNNRTVSIDNLKPTSHQ 375
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367

Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee..........eeeeeee.....eeeeee...hhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh........hhhhhhhh...............hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uop B 116 DRPQKPFDKFFIDYIGPLPPSQGYLYVLVVVDGMTGFTWLYPTKAPSTSATVKSLNVLTSIAIPKVIHSDQGAAFTSSTFAEWAKERGIHLEFSTPYHPQSSGKVERKNSDIKRLLTKLLVGRPTKWYDLLPVVQLALNNTYSPVLKYTPHQLLFGIDSNTPFANQDTLDLTREEELSLLQEIR 299
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295

Chain C from PDB  Type:DNA  Length:19
                                                   
                 5uop C   1 ATTGTCATGGAATTTCGCA  19
                                    10

Chain D from PDB  Type:DNA  Length:17
                                                 
                 5uop D   1 TGCGAAATTCCATGACA  17
                                    10

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 5UOP)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		8G4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Gly A:131 - Pro A:132	[ RasMol ]
		Gly B:131 - Pro B:132	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	5uop
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		Orientation in Membranes	:	OPM
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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Gene Ontology (28, 28)

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