5HRN - JenaLib

Asymmetric Unit

Asym. Unit - sites

Biological Unit 1

Biol. Unit 1 - sites

collapse

expand

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Description

Title :   HIV INTEGRASE CATALYTIC DOMAIN CONTAINING F185K MUTATION COMPLEXED WITH GSK0002

Authors :   R. T. Nolte

Date :   23 Jan 16 (Deposition) - 14 Dec 16 (Release) - 21 Dec 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.75

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

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

Reference :   K. Gupta, V. Turkki, S. Sherrill-Mix, Y. Hwang, G. Eilers, L. Taylor, C. Mcdanal, P. Wang, D. Temelkoff, R. T. Nolte, E. Velthuisen, J. Jeffrey, G. D. Van Duyne, F. D. Bushman
Structural Basis For Inhibitor-Induced Aggregation Of Hiv Integrase.
Plos Biol. V. 14 02584 2016
PubMed-ID: 27935939 | Reference-DOI: 10.1371/JOURNAL.PBIO.1002584

Compounds

Molecule 1 - INTEGRASE
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET24
	Expression System Strain	:	BL21STAR(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GAG-POL
	Mutation	:	YES
	Organism Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

Structural Features

Chains, Units

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 6)

Asymmetric Unit (4, 6)

No.	Name	Count	Type	Full Name
1	65P	1	Ligand/Ion	(2S)-TERT-BUTOXY[1-(3,4-DIFLUOROBENZYL)-6-METHYL-4-(5-METHYL-3,4-DIHYDRO-2H-CHROMEN-6-YL)-1H-PYRROLO[2,3-B]PYRIDIN-5-YL]ACETIC ACID
2	CAC	2	Ligand/Ion	CACODYLATE ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	65P	2	Ligand/Ion	(2S)-TERT-BUTOXY[1-(3,4-DIFLUOROBENZYL)-6-METHYL-4-(5-METHYL-3,4-DIHYDRO-2H-CHROMEN-6-YL)-1H-PYRROLO[2,3-B]PYRIDIN-5-YL]ACETIC ACID
2	CAC	4	Ligand/Ion	CACODYLATE ION
3	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	2	Ligand/Ion	SULFATE ION

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:65 , GLU A:92 , THR A:97 , ASN A:120	binding site for residue CAC A 301
2	AC2	SOFTWARE	CYS A:130 , ILE A:135 , LYS A:136 , GLN A:137	binding site for residue CAC A 302
3	AC3	SOFTWARE	LYS A:71 , GLU A:170 , HIS A:171 , LEU A:172 , HOH A:412 , HOH A:481	binding site for residue SO4 A 303
4	AC4	SOFTWARE	ALA A:105 , GLY A:106 , TRP A:108 , PRO A:109 , ASN A:184 , LYS A:185 , GLY A:197 , HOH A:449 , HOH A:482	binding site for residue EDO A 304
5	AC5	SOFTWARE	GLU A:69 , GLY A:163 , HOH A:442	binding site for residue EDO A 305
6	AC6	SOFTWARE	LEU A:102 , THR A:125 , ALA A:129 , TRP A:132 , GLN A:168 , ALA A:169 , GLU A:170 , HIS A:171 , THR A:174 , HOH A:427 , HOH A:483 , HOH A:498	binding site for residue 65P A 306

SS Bonds (0, 0)

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

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 5HRN)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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

PROSITE Motifs (0, 0)

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

Exons (0, 0)

(no "Exon" information available for 5HRN)

Sequences/Alignments

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:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeee.....eeeeee...hhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hrn A  57 SPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTIHTDNGSNFTSATVKAACWWAGIKQEFGIPYNPQSQGVVESMNKELKKIIGQVRDQAEHLKTAVQMAVFIHNKKRKGYSAGERIVDIIATDI 208
                                    66        76        86        96       106       116       126       136       146       156       166       176       186 ||    200        
                                                                                                                                                             188|               
                                                                                                                                                              193

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

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

CATH Domains (0, 0)

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

Pfam Domains (0, 0)

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

Gene Ontology (59, 59)

Asymmetric Unit(hide GO term definitions)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		65P	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CAC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EDO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5hrn)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	5hrn
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	POL_HV1H2 \| P04585
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	POL_HV1H2 \| P04585
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	POL_HV1H2 \| P04585	:	1a30 1bv7 1bv9 1bve 1bvg 1bwa 1bwb 1c0t 1c0u 1c1b 1c1c 1dmp 1dtq 1dtt 1e6j 1ep4 1esk 1ex4 1exq 1fb7 1fk9 1fko 1fkp 1g6l 1hiv 1hvh 1hvr 1hwr 1hxb 1jkh 1jla 1jlb 1jlc 1jle 1jlf 1jlg 1jlq 1klm 1lv1 1lw0 1lw2 1lwc 1lwe 1lwf 1ncp 1o1w 1odw 1odx 1ody 1qbr 1qbs 1qbt 1qbu 1rev 1rt1 1rt2 1rt3 1rt4 1rt5 1rt6 1rt7 1rtd 1rth 1rti 1rtj 1s1t 1s1u 1s1v 1s1w 1s1x 1t05 1tam 1tkt 1tkx 1tkz 1tl1 1tl3 1vrt 1vru 2hnd 2hny 2hnz 2kod 2nph 2opp 2opq 2opr 2ops 2rf2 2rki 2whh 2wom 2won 2ynf 2yng 2ynh 2yni 3ao2 3c6t 3c6u 3di6 3dle 3dlg 3dm2 3dmj 3dok 3dol 3dox 3drp 3drr 3drs 3dya 3e01 3ffi 3i0r 3i0s 3kjv 3kk1 3kk2 3kk3 3kt2 3kt5 3lak 3lal 3lam 3lan 3lp0 3lp1 3lp2 3m8p 3m8q 3mec 3med 3mee 3meg 3mim 3n3i 3nbp 3phv 3qin 3qio 3qip 3t19 3t1a 3tam 4b3o 4b3p 4b3q 4i7f 4kse 4kv8 4ncg 4q1w 4q1x 4q1y 4q5m 4qlh 4u1h 4u1i 4u1j 4u7q 4u7v 5dgu 5dgw 5eu7 5hrp 5hrr 5hrs 5im7 5j2m 5j2n 5j2p 5j2q 5k14 5t82

Related Entries Specified in the PDB File

5hot 5hrp 5hrr 5hrs