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(-) Description

Title :  CRYSTAL STRUCTURE OF INACTIVE SINGLE CHAIN VARIANT OF HIV-1 PROTEASE IN COMPLEX WITH THE SUBSTRATE P2-NC
 
Authors :  C. A. Schiffer, S. Mittal
Date :  17 Apr 12  (Deposition) - 06 Jun 12  (Release) - 09 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,P
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 P2-NC
    Chains: P
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Other Details: SYNTHETIC PEPTIDE CORRESPONDING TO P2-NC CLEAVAGE SITE FOR HIV-1 PROTEASE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AP

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3EDO3Ligand/Ion1,2-ETHANEDIOL
4GOL3Ligand/IonGLYCEROL
5PO41Ligand/IonPHOSPHATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:108 , HOH A:326BINDING SITE FOR RESIDUE BME A 201
02AC2SOFTWAREGLY A:168 , HIS A:169 , LYS A:170BINDING SITE FOR RESIDUE EDO A 202
03AC3SOFTWARETRP A:6 , ARG A:48 , ASP A:129 , ARG A:187 , ASN A:188 , HOH A:369BINDING SITE FOR RESIDUE GOL A 203
04AC4SOFTWARELYS A:7 , ARG A:8 , ARG A:187BINDING SITE FOR RESIDUE EDO A 204
05AC5SOFTWAREILE A:54 , THR A:91 , GLN A:92 , GLY A:149 , GLY A:151BINDING SITE FOR RESIDUE ACT A 205
06AC6SOFTWAREVAL A:111 , THR A:112 , TRP A:142BINDING SITE FOR RESIDUE EDO A 206
07AC7SOFTWAREARG A:114 , TRP A:142 , PRO A:144 , LYS A:145 , LYS A:155 , VAL A:156 , GLU A:165BINDING SITE FOR RESIDUE GOL A 207
08AC8SOFTWARETHR A:4 , LEU A:5 , TRP A:6 , GLY A:51 , THR A:191 , MET A:195 , HOH A:359BINDING SITE FOR RESIDUE GOL A 208
09AC9SOFTWAREGLY A:16 , PRO A:63 , ARG A:114 , GLY A:116 , GLY A:117 , HOH A:347 , HOH A:382BINDING SITE FOR RESIDUE PO4 A 209
10BC1SOFTWAREARG A:8 , LEU A:23 , ASN A:25 , GLY A:27 , SER A:28 , ASP A:29 , PHE A:30 , LYS A:45 , ILE A:47 , ARG A:48 , VAL A:82 , ASN A:125 , GLY A:127 , SER A:128 , ASP A:129 , ASP A:130 , THR A:180 , HOH A:312 , HOH P:101BINDING SITE FOR CHAIN P OF SUBSTRATE P2-NC

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EQ0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EQ0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EQ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EQ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4EQ0)

(-) 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.....eeehhhhhh....eee..........eeeeee..eeeeeee......eee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4eq0 A   1 PQITLWKRPLVTIRIGGQLKEALLNTGSDFTVLEEMNLPGKWKPKMIRGIGGFIKVRQYDQIPVEILGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNFPQITLWKRPLVTIRIGGQLKEALLNTGSDDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQIPVEILGHKAIGTVLVGPTPVNIIGRNLLTQIGMTLNF 199
                                    10        20        30        40        50        60        70        80        90       101       111       121       131       141       151       161       171       181       191        
                                                                                                                             99|                                                                                                  
                                                                                                                             101                                                                                                  


Chain P 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
                 4eq0 P   2 ATIMMQR   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)

(no "SCOP Domain" information available for 4EQ0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EQ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EQ0)

(-) Gene Ontology  (47, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  Q9YP46_9HIV1 | Q9YP46
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        POL_HV1A2 | P03369: 1aid 1b6j 1b6k 1b6l 1b6m 1b6p 1cpi 1d4k 1d4l 1f7a 1kj4 1kj7 1kjf 1kjg 1kjh 1kzk 1mt7 1mt8 1mt9 1mtb 1mtr 1n49 1t3r 1tsq 1tsu 1ytg 1yth 1z1h 1z1r 2aid 2f3k 2fgu 2fgv 2fns 2fnt 2j9j 2j9k 2je4 2nxd 2nxl 2nxm 2q3k 2qhy 2qhz 2qi0 2qi1 2qi3 2qi4 2qi5 2qi6 2qi7 3aid 3bxr 3bxs 3ekp 3ekq 3ekt 3ekv 3ekw 3ekx 3eky 3el0 3el1 3el4 3el5 3el9 3em3 3em4 3em6 3fsm 3gi0 3gi4 3gi5 3gi6 3hau 3haw 3hbo 3hdk 3hlo 3hvp 3hzc 3i2l 3i7e 3iaw 3ka2 3lzv 3mxd 3mxe 3nwq 3nwx 3nxn 3nyg 3o9f 3o9g 3o9h 3o9i 3oxv 3oxw 3oxx 3oy4 3r4b 4ep2 4ep3 4epj 4eqj 4f73 4f74 4f75 4f76 4hvp 4obd 4obf 4obg 4obh 4obj 4obk 4qj2 4qj6 4qj7 4qj8 4qj9 4qja 7hvp 8hvp
        Q9YP46_9HIV1 | Q9YP46: 2l45 2l46 3oua 3ouc 3p9g 3p9h
UniProtKB/TrEMBL
        Q9YP46_9HIV1 | Q9YP46: 2l44 4ep3 4epj 4fae

(-) Related Entries Specified in the PDB File

4ep2 4ep3 4epj 4eqj