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(-) Description

Title :  HIV-1 PROTEASE COMPLEXED WITH GEM-DIOL-AMINE TETRAHEDRAL INTERMEDIATE
 
Authors :  Y. F. Tie, C. H. Shen, I. T. Weber
Date :  14 Jun 12  (Deposition) - 17 Oct 12  (Release) - 17 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Hydrolase, Catalytic Mechanism, Drug Resistance, Aspartic Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. H. Shen, Y. Tie, X. Yu, Y. F. Wang, A. Y. Kovalevsky, R. W. Harrison, I. T. Weber
Capturing The Reaction Pathway In Near-Atomic-Resolution Crystal Structures Of Hiv-1 Protease.
Biochemistry V. 51 7726 2012
PubMed-ID: 22963370  |  Reference-DOI: 10.1021/BI3008092

(-) Compounds

Molecule 1 - HIV-1 PROTEASE
    Chains: A, B
    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
    Mutation: YES
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Synonym: PR, RETROPEPSIN
 
Molecule 2 - HEPTAPEPTIDE
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 3 - HEPTAPEPTIDE
    Chains: D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1CL5Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3IL02Mod. Amino Acid(2S,3S)-2-AMINO-3-METHYLPENTANE-1,1-DIOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:74 , ASN A:88 , HOH A:1052 , ARG B:41BINDING SITE FOR RESIDUE CL A 101
2AC2SOFTWAREARG A:8 , HOH A:1091BINDING SITE FOR RESIDUE CL A 102
3AC3SOFTWAREGLN A:18 , SER A:37 , HOH A:1029BINDING SITE FOR RESIDUE CL A 103
4AC4SOFTWAREARG A:8 , LEU A:10 , VAL A:82 , HOH A:1090 , HOH A:1091 , GLN D:361 , HOH D:404BINDING SITE FOR RESIDUE GOL A 104
5AC5SOFTWARETRP B:6BINDING SITE FOR RESIDUE CL B 501
6AC6SOFTWARETHR B:74 , ASN B:88 , HOH B:606 , HOH B:691BINDING SITE FOR RESIDUE CL B 502
7AC7SOFTWAREGLU B:35 , LYS B:55 , ARG B:57 , VAL B:77 , GLY B:78BINDING SITE FOR RESIDUE GOL B 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FL8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FL8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FL8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FL8)

(-) Exons   (0, 0)

(no "Exon" information available for 4FL8)

(-) 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 d4fl8a_ A: 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......eehhhhhhhhh.eee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4fl8 A   1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF  99
                                    10        20        30        40        50        60        70        80        90         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains d4fl8b_ 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
                 4fl8 B   1 PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYDQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF  99
                                    10        20        30        40        50        60        70        80        90         


Chain C from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....ee. Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4fl8 C 261 QIxIEIA 267
                              |    
                            263-IL0


Chain D from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author .eee... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 4fl8 D 359 YDQIxIE 365
                                |  
                              363-IL0
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FL8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FL8)

(-) Gene Ontology  (45, 45)

Asymmetric/Biological Unit(hide GO term definitions)

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  4fl8
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  POL_HV1BR | P03367
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  3.4.23.16
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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 4flg 4fm6 4gb2 4hdb 4hdf 4hdp 4he9 4heg 4hla 4j54 4j55 4j5j 4jec 4ll3 5e5k 7upj

(-) Related Entries Specified in the PDB File

3b7v 3b80 4flg 4fm6