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(-) Description

Title :  HIV-1 PROTEASE (MUTANT Q7K L33I L63I) IN COMPLEX WITH A BICYCLIC PYRROLIDINE INHIBITOR
 
Authors :  M. Stieler, A. Heine, G. Klebe
Date :  26 Jul 12  (Deposition) - 31 Jul 13  (Release) - 31 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dimer, Aspartyl Protease, Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Stieler, N. Klee, A. Heine, S. Doerr, W. Diederich, G. Klebe
Cocrystallization Of Potent Pyrrolidine Based Hiv-1 Proteas Inhibitors
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GAG-POL POLYPROTEIN
    Chains: A, B
    EC Number: 3.4.23.16, 2.7.7.49, 2.7.7.7, 3.1.26.13, 3.1.13.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 501-599
    Gene: GAG-POL
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (BRU ISOLATE)
    Organism Taxid: 11686
    Synonym: PR160GAG-POL, MATRIX PROTEIN P17, MA, CAPSID PROTEIN P24, CA, SPACER PEPTIDE P2, NUCLEOCAPSID PROTEIN P7, NC, TRANSFRAME PEPTIDE, TF, P6-POL, P6*, PROTEASE, PR, RETROPEPSIN, REVERSE TRANSCRIPTASE/RIBONUCLEASE H, EXORIBONUCLEASE H, P66 RT, P51 RT, P15, INTEGRASE, IN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
10LQ1Ligand/Ion(4AS,7AS)-1,4-BIS(DIPHENYLMETHYL)HEXAHYDRO-1H-PYRROLO[3,4-B]PYRAZINE-2,3-DIONE
2CL3Ligand/IonCHLORIDE ION
3GOL2Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:73 , THR A:74 , ASN A:88 , HOH A:235 , HOH A:287 , ARG B:41BINDING SITE FOR RESIDUE CL A 101
2AC2SOFTWARELYS A:70 , HOH A:262 , HOH A:289 , GLY B:40 , HOH B:212BINDING SITE FOR RESIDUE GOL A 102
3AC3SOFTWAREGLN A:18 , SER A:37 , HOH A:261 , THR B:12 , LYS B:14 , LEU B:19 , GLU B:65 , ILE B:66 , CYS B:67 , GLY B:68BINDING SITE FOR RESIDUE GOL A 103
4AC4SOFTWAREASP A:25 , GLY A:27 , ALA A:28 , GLY A:48 , ILE A:50 , VAL A:82 , ASP B:25 , GLY B:27 , ALA B:28 , ASP B:29 , GLY B:48 , GLY B:49 , ILE B:50 , PRO B:81BINDING SITE FOR RESIDUE 0LQ B 101
5AC5SOFTWAREGLY B:73 , THR B:74 , ASN B:88 , HOH B:207BINDING SITE FOR RESIDUE CL B 102
6AC6SOFTWARETRP B:6BINDING SITE FOR RESIDUE CL B 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4GB2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GB2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4GB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4GB2)

(-) Exons   (0, 0)

(no "Exon" information available for 4GB2)

(-) 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:99
                                                                                                                                  
               SCOP domains d4gb2a_ A: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee........eeeeeeee..eeeeeeeeeeeeeee..eeeeeeeee.....eeehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4gb2 A  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d4gb2b_ B: Human immunodeficiency virus type 1 protease                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eeeeee..eeeeeee.......ee.........eeeeeee..eeeeeeeeeeeeeee..eeeeeeeee......eehhhhhh....eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  4gb2 B  1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF 99
                                    10        20        30        40        50        60        70        80        90
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4GB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4GB2)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  4gb2
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  POL_HV1BR | P03367
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 Related Entries

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

UniProtKB/Swiss-Prot
        POL_HV1BR | P03367: 1a8g 1a8k 1a94 1aaq 1d4s 1d4y 1daz 1dif 1fqx 1hhp 1hni 1hpo 1hpx 1hsg 1hvl 1iiq 1izi 1lzq 1m0b 1mrw 1mrx 1msm 1msn 1nh0 1rl8 1sdt 1sdu 1sdv 1sgu 1sh9 1sp5 1u8g 1upj 1xl2 1xl5 1z8c 1zbg 1zj7 1zlf 1zpk 1zsf 1zsr 1ztz 2a1e 2az8 2az9 2azb 2azc 2b7z 2bb9 2fde 2fnd 2hb2 2hb4 2hc0 2hnd 2hny 2ien 2o4k 2o4l 2o4n 2o4p 2o4s 2p3b 2pk5 2pk6 2pqz 2pwc 2pwr 2pym 2pyn 2q63 2q64 2qak 2qci 2qd6 2qd7 2qd8 2qhc 2qnn 2qnp 2qnq 2r43 2upj 2z4o 2zga 2zye 3a2o 3bc4 3bgb 3bgc 3bhe 3bva 3bvb 3ckt 3djk 3dk1 3fx5 3ggu 3h5b 3i6o 3i8w 3jvw 3jvy 3jw2 3kdb 3kdc 3kdd 3ndu 3ndw 3ndx 3nls 3psu 3pwm 3pwr 3qbf 3qih 3qn8 3qp0 3qpj 3qrm 3qro 3qrs 3st5 3t11 3t3c 3tkg 3tkw 3tl9 3tof 3tog 3toh 3ttp 3u7s 3ucb 3uf3 3ufn 3uhl 3vf5 3vf7 3vfb 4dfg 4faf 4fe6 4fl8 4flg 4fm6 4hdb 4hdf 4hdp 4he9 4heg 4hla 4j54 4j55 4j5j 4jec 4ll3 5e5k 7upj

(-) Related Entries Specified in the PDB File

3qih THE SAME PROTEIN COMPLEXED WITH A BICYCLIC PYRROLIDINE.
3qn8 THE SAME PROTEIN COMPLEXED WITH A BICYCLIC PYRROLIDINE.
3qp0 THE SAME PROTEIN COMPLEXED WITH A BICYCLIC PYRROLIDINE.