4EP2 - JenaLib

Title :   CRYSTAL STRUCTURE OF INACTIVE SINGLE CHAIN WILD-TYPE HIV-1 PROTEASE IN COMPLEX WITH THE SUBSTRATE RT-RH

Authors :   C. A. Schiffer, S. Mittal

Date :   16 Apr 12 (Deposition) - 06 Jun 12 (Release) - 09 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Hiv-1 Protease, Specificity Design, Drug Design, Protease Inhibitors, Aids, Aspartyl Protease, Hydrolase, Hydrolase-Hydrolase Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   O. Alvizo, S. Mittal, S. L. Mayo, C. A. Schiffer
Structural, Kinetic, And Thermodynamic Studies Of Specificity Designed Hiv-1 Protease.
Protein Sci. V. 21 1029 2012
PubMed-ID: 22549928 | Reference-DOI: 10.1002/PRO.2086

Compounds

Molecule 1 - PROTEASE, TETHERED DIMER
	Chains	:	A
	EC Number	:	3.4.23.16
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GAG-POL
	Organism Common	:	HIV-1
	Organism Taxid	:	11685
	Strain	:	SF2

Molecule 2 - SUBSTRATE RT-RH
	Chains	:	B
	Engineered	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Other Details	:	THIS PEPTIDE REPRESENTS THE RT-RH SUBSTRATE CLEAVAGE SITE FOR HIV PROTEASE
	Synthetic	:	YES

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:120 , GLU A:121 , GLU A:134 , ASN A:183	BINDING SITE FOR RESIDUE GOL A 201
2	AC2	SOFTWARE	GLY A:16 , PRO A:63 , GLY A:116 , GLY A:117 , HOH A:304 , HOH A:315 , HOH A:354	BINDING SITE FOR RESIDUE PO4 A 202
3	AC3	SOFTWARE	ARG A:8 , ASN A:25 , GLY A:27 , ALA A:28 , ASP A:29 , ASP A:30 , ILE A:47 , GLY A:48 , GLY A:49 , ILE A:50 , PRO A:81 , VAL A:82 , ARG A:108 , LEU A:123 , ASN A:125 , GLY A:127 , ALA A:128 , ASP A:129 , ASP A:130 , ILE A:147 , GLY A:148 , GLY A:149 , ILE A:150 , PRO A:181 , VAL A:182 , ILE A:184 , HOH B:101 , HOH B:102 , HOH B:103	BINDING SITE FOR CHAIN B OF SUBSTRATE RT-RH

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

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:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee..........eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ep2 A   1 PQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEILGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNFPQITLWKRPLVTIRIGGQLKEALLNTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEILGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNF 199
                                    10        20        30        40        50        60        70        80        90       101       111       121       131       141       151       161       171       181       191        
                                                                                                                             99|                                                                                                  
                                                                                                                             101

Chain B from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4ep2 B   2 AETFYVD   8

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)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (45, 68)

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	Sites
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Description