3VU6 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   SHORT PEPTIDE HIV ENTRY INHIBITOR MT-SC22EK WITH A M-T HOOK

Authors :   X. Yao, H. H. Chong, S. Waltersperger, M. T. Wang, Y. X. He, S. Cui

Date :   19 Jun 12 (Deposition) - 19 Dec 12 (Release) - 24 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.32

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (3x)

Keywords :   6-Helix Bundle, Coiled-Coil, Membrane, Fusion Inhibitor, M-T Hook, Hiv Entry, Membrane Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. H. Chong, X. Yao, Z. Qiu, J. Sun, M. Zhang, S. Waltersperger, M. T. Wang, S. -L. Liu, S. Cui, Y. X. He
Short-Peptide Fusion Inhibitors With High Potency Against Wild-Type And Enfuvirtide-Resistant Hiv-1
Faseb J. V. 27 1203 2013
PubMed-ID: 23233535 | Reference-DOI: 10.1096/FJ.12-222547

Molecule 1 - TRANSMEMBRANE PROTEIN GP41
	Chains	:	A
	Fragment	:	UNP RESIDUES 553-590
	Organism Common	:	HIV-1
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676

Molecule 2 - MTSC22
	Chains	:	B
	Engineered	:	YES
	Other Details	:	SEQUENCE OF MTSC22 DOES NOT OCCUR NATURALLY IN HIV-1, BUT DESIGNED BASED ON SEQUENCE OF HIV-1 GP41 CHR
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	ACE	1	Mod. Amino Acid	ACETYL GROUP
2	NH2	1	Mod. Amino Acid	AMINO GROUP
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 9)

No.	Name	Count	Type	Full Name
1	ACE	3	Mod. Amino Acid	ACETYL GROUP
2	NH2	3	Mod. Amino Acid	AMINO GROUP
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:585 , LYS A:588	BINDING SITE FOR RESIDUE SO4 A 601
2	AC2	SOFTWARE	ASN A:553 , ASN A:554 , LEU A:555 , LEU A:556 , GLU A:560 , ALA A:561 , GLN A:563 , HIS A:564 , LEU A:565 , GLN A:567 , LEU A:568 , TRP A:571 , GLY A:572 , LYS A:574 , ARG A:579 , HOH A:705 , HOH A:722 , HOH A:737	BINDING SITE FOR CHAIN B OF MTSC22

(no "SS Bond" information available for 3VU6)

(no "Cis Peptide Bond" information available for 3VU6)

(no "SAP(SNP)/Variant" information available for 3VU6)

(no "PROSITE Motif" information available for 3VU6)

(no "Exon" information available for 3VU6)

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:39
 aligned with ENV_HV1B1 | P03375 from UniProtKB/Swiss-Prot  Length:856

    Alignment length:39
                                   562       572       582         
            ENV_HV1B1   553 NNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQQ 591
               SCOP domains --------------------------------------- SCOP domains
               CATH domains --------------------------------------- CATH domains
               Pfam domains --------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------- PROSITE
                 Transcript --------------------------------------- Transcript
                 3vu6 A 553 NNLLRAIEAQQHLLQLTVWGIKQLQARILAVERYLKDQx 591
                                   562       572       582        |
                                                                591-NH2

Chain B from PDB  Type:PROTEIN  Length:25
                                                         
               SCOP domains ------------------------- SCOP domains
               CATH domains ------------------------- CATH domains
               Pfam domains ------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------- SAPs(SNPs)
                    PROSITE ------------------------- PROSITE
                 Transcript ------------------------- Transcript
                 3vu6 B 625 xMTWEEWDKKIEEYTKKIEELIKKS 649
                            |      634       644     
                            |                        
                          625-ACE

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 3VU6)

(no "CATH Domain" information available for 3VU6)

(no "Pfam Domain" information available for 3VU6)

Asymmetric Unit(hide GO term definitions)

Chain A (ENV_HV1B1 | P03375)

molecular function
	GO:0042609	CD4 receptor binding	Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0032403	protein complex binding	Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075512	clathrin-dependent endocytosis of virus by host cell	Any clathrin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins by invagination of a specific region of the host cell plasma membrane around the bound virus to form a clathrin-coated pit, which then pinches off to form a clathrin-coated endocytic vesicle containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039654	fusion of virus membrane with host endosome membrane	Fusion of a virus membrane with a host endosome membrane. Occurs after internalization of the virus through the endosomal pathway, and results in release of the virus contents into the cell.
	GO:0019064	fusion of virus membrane with host plasma membrane	Fusion of a viral membrane with the host cell membrane during viral entry. Results in release of the virion contents into the cytoplasm.
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0002223	stimulatory C-type lectin receptor signaling pathway	Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019082	viral protein processing	Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a viral protein.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0044220	host cell perinuclear region of cytoplasm	The host cell cytoplasm situated near, or occurring around, the host nucleus.
	GO:0044538	host cell periphery	The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures of a host cell.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

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
		ACE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NH2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3vu6)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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)

Access by PDB/NDB ID
	3vu6
		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
	ENV_HV1B1 \| P03375
		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

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
	ENV_HV1B1 \| P03375
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ENV_HV1B1 \| P03375	:	2ari 3vgx 3vgy 3vh7 3vu5 3w19

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (26, 26)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File