2Q7C - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF IQN17

Authors :   V. N. Malashkevich, D. M. Eckert, L. H. Hong, P. S. Kim

Date :   06 Jun 07 (Deposition) - 19 Jun 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C

Keywords :   Envelope Glycoprotein, Coiled Coil, Viral Protein/Viral Protein Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. M. Eckert, V. N. Malashkevich, L. H. Hong, P. A. Carr, P. S. Kim
Inhibiting Hiv Entry: Discovery Of D-Peptide Inhibitors That Target The Gp41 Coiled-Coil Pocket
Cell(Cambridge, Mass. ) V. 99 103 1999
PubMed-ID: 10520998 | Reference-DOI: 10.1016/S0092-8674(00)80066-5
(for further references see the PDB file header)

Molecule 1 - FUSION PROTEIN BETWEEN YEAST VARIANT GCN4 AND HIVGP41
	Chains	:	A, B, C
	Engineered	:	YES
	Other Details	:	SYNTHETIC PEPTIDE. THE SEQUENCE NATURALLY OCCURS IN SACCHAROMYCES CEREVISIAE AND HUMAN IMMUNODEFICIENCY VIRUS.
	Synonym	:	IQN17
	Synthetic	:	YES

		1	2	3
Asymmetric/Biological Unit	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	ACE	3	Mod. Amino Acid	ACETYL GROUP
2	CL	4	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:16 , GLN B:16 , GLN C:16	BINDING SITE FOR RESIDUE CL A 201
2	AC2	SOFTWARE	ARG B:1 , ARG B:43 , LYS C:3 , HOH C:234	BINDING SITE FOR RESIDUE CL B 202
3	AC3	SOFTWARE	LYS A:3 , ARG C:1 , ARG C:43	BINDING SITE FOR RESIDUE CL C 203
4	AC4	SOFTWARE	ARG A:1 , ARG A:43 , ACE B:0	BINDING SITE FOR RESIDUE CL A 204

(no "SS Bond" information available for 2Q7C)

(no "Cis Peptide Bond" information available for 2Q7C)

(no "SAP(SNP)/Variant" information available for 2Q7C)

(no "PROSITE Motif" information available for 2Q7C)

(no "Exon" information available for 2Q7C)

Asymmetric/Biological 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:46
 aligned with A3F986_9HIV1 | A3F986 from UniProtKB/TrEMBL  Length:858

    Alignment length:164
                                   429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579    
         A3F986_9HIV1   420 CRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGNTENKTEVFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGAMFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAIEAQQKLLQLTVWGIKQLQARIL 583
               SCOP domains -d2q7c                                      a1                        A:1-4      5                                                                                   SCOP domains
               CATH domains -2q7cA                                      00                        A:1-4      5                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh--------------------------------------hh-----------------------hhhhhh------hhhhh--hhhh-------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7c A   0 xRMKQI--------------------------------------ED-----------------------KIEEIE------SKQKK--IENE-------------------------------------------------IARIKKLLQLTVWGIKQLQARIL  45
                            |    |   -         -         -         -    ||   -         -         8    |    - |   |  20 |       -         -         -         -         - |      31        41    
                            |    5                                      6|                       8   13     14  18 19 22                                                23                      
                            0-ACE                                        7

Chain B from PDB  Type:PROTEIN  Length:46
 aligned with A3F986_9HIV1 | A3F986 from UniProtKB/TrEMBL  Length:858

    Alignment length:164
                                   429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579    
         A3F986_9HIV1   420 CRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGNTENKTEVFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGAMFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAIEAQQKLLQLTVWGIKQLQARIL 583
               SCOP domains -d2q7c                                      b1                        B:1-4      5                                                                                   SCOP domains
               CATH domains -2q7cB                                      00                        B:1-4      5                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh--------------------------------------hh-----------------------hhhhhh------hhhhh--hhhh-------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7c B   0 xRMKQI--------------------------------------ED-----------------------KIEEIE------SKQKK--IENE-------------------------------------------------IARIKKLLQLTVWGIKQLQARIL  45
                            |    |   -         -         -         -    ||   -         -         8    |    - |   |  20 |       -         -         -         -         - |      31        41    
                            0-ACE5                                      6|                       8   13     14  18 19 22                                                23                      
                                                                         7

Chain C from PDB  Type:PROTEIN  Length:46
 aligned with A3F986_9HIV1 | A3F986 from UniProtKB/TrEMBL  Length:858

    Alignment length:164
                                   429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579    
         A3F986_9HIV1   420 CRIKQIINMWQEVGKAMYAPPIRGQIRCSSNITGLLLTRDGGNTENKTEVFRPGGGNMKDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQREKRAVGIGAMFLGFLGAAGSTMGAASMTLTVQARQLLSGIVQQQSNLLRAIEAQQKLLQLTVWGIKQLQARIL 583
               SCOP domains -d2q7c                                      c1                        C:1-4      5                                                                                   SCOP domains
               CATH domains -2q7cC                                      00                        C:1-4      5                                                                                   CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------GP41-2q7cC01       Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------GP41-2q7cC02       Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------GP41-2q7cC03       Pfam domains (3)
         Sec.struct. author .hhhhh--------------------------------------hh-----------------------hhhhhh------hhhhh--hhhh-------------------------------------------------hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2q7c C   0 xRMKQI--------------------------------------ED-----------------------KIEEIE------SKQKK--IENE-------------------------------------------------IARIKKLLQLTVWGIKQLQARIL  45
                            |    |   -         -         -         -    ||   -         -         8    |    - |   |  20 |       -         -         -         -         - |      31        41    
                            0-ACE5                                      6|                       8   13     14  18 19 22                                                23                      
                                                                         7

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Coiled coil proteins (689)

Fold: Stalk segment of viral fusion proteins (231)

Superfamily: Virus ectodomain (48)

Family: Virus ectodomain (44)

Protein domain: Retrovius gp41 protease-resistant core (35)

Human immunodeficiency virus type 1 [TaxId: 11676] (23)

1a	d2q7ca1	A:1-45
1b	d2q7cb1	B:1-45
1c	d2q7cc1	C:1-45

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Single alpha-helices involved in coiled-coils or other helix-helix interfaces (552)

Homologous Superfamily: [code=1.20.5.170, no name defined] (60)

[unclassified] (20)

1a	2q7cA00	A:1-45
1b	2q7cB00	B:1-45
1c	2q7cC00	C:1-45

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: GP41] (22)

Family: GP41 (22)

Human immunodeficiency virus 1 (10)

1a	GP41-2q7cC01	C:28-45
1b	GP41-2q7cC02	C:28-45
1c	GP41-2q7cC03	C:28-45

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C (A3F986_9HIV1 | A3F986)

molecular function
	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: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: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: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: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/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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