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(-) Description

Title :  STRUCTURE OF THE NATIVE FULL-LENGTH HIV-1 CAPSID PROTEIN IN COMPLEX WITH PF-3450074 (PF74)
 
Authors :  A. T. Gres, K. A. Kirby, S. G. Sarafianos
Date :  29 Dec 14  (Deposition) - 10 Jun 15  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Capsid Protein, Pf-3450074, Pf74, Complex, Antiviral, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. T. Gres, K. A. Kirby, V. N. Kewalramani, J. J. Tanner, O. Pornillos, S. G. Sarafianos
Structural Virology. X-Ray Crystal Structures Of Native Hiv-1 Capsid Protein Reveal Conformational Variability.
Science V. 349 99 2015
PubMed-ID: 26044298  |  Reference-DOI: 10.1126/SCIENCE.AAA5936

(-) Compounds

Molecule 1 - HIV-1 CAPSID PROTEIN
    Chains: A
    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
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 GROUP M SUBTYPE B (ISOLATE NY5)
    Organism Taxid: 11698
    Strain: ISOLATE NY5
    Synonym: PR55GAG

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
11B01Ligand/IonN-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
2CL2Ligand/IonCHLORIDE ION
3IOD6Ligand/IonIODIDE ION
Biological Unit 1 (2, 42)
No.NameCountTypeFull Name
11B06Ligand/IonN-METHYL-NALPHA-[(2-METHYL-1H-INDOL-3-YL)ACETYL]-N-PHENYL-L-PHENYLALANINAMIDE
2CL-1Ligand/IonCHLORIDE ION
3IOD36Ligand/IonIODIDE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:173binding site for residue IOD A 301
2AC2SOFTWAREGLN A:95 , GLY A:156 , PRO A:157 , LYS A:158binding site for residue IOD A 302
3AC3SOFTWAREARG A:18binding site for residue IOD A 304
4AC4SOFTWAREGLN A:179binding site for residue CL A 307
5AC5SOFTWAREASN A:57binding site for residue CL A 308
6AC6SOFTWAREASN A:53 , LEU A:56 , ASN A:57 , GLN A:63 , MET A:66 , LYS A:70 , ALA A:105 , TYR A:130 , ARG A:173binding site for residue 1B0 A 309

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:198 -A:218

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asn A:121 -Pro A:122

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XFZ)

(-) Sequences/Alignments

Asymmetric 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:213
                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhh...hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...............hhhhhh....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhh......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhhhhhhh.....hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xfz A   1 PIVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVGGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQEVKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGV 221
                              ||    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218   
                              3|                                                                                                                                                                                                                 
                              12
   Legend:   → Mismatch (orange background)
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  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 4XFZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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  4xfz
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  GAG_HV1N5 | P12493
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 Related Entries

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

UniProtKB/Swiss-Prot
        GAG_HV1N5 | P12493: 1gwp 1hiw 1uph 2c55 2x2d 3gv2 4u0a 4u0b 4u0c 4u0d 4u0e 4u0f 4xfx 4xfy 4xro 4xrq 5hgl 5hgm 5hgn 5hgo 5hgp 5irt 5jpa 5l93 5o2u 5upw

(-) Related Entries Specified in the PDB File

4xfx SAME PROTEIN WITHOUT ANY POST-CRYSTALLIZATION TREATMENT
4xfy SAME PROTEIN, DEHYDRATED