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(-) Description

Title :  CRYSTAL STRUCTURE OF UNLIGANDED HIV-1 CLADE C STRAIN ZM109F.PB4 GP120 CORE
 
Authors :  Y. D. Kwon, P. D. Kwong
Date :  20 Aug 11  (Deposition) - 04 Apr 12  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Hiv-1 Gp120, Unliganded, Clade C Zm109F. Pb4, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. D. Kwon, A. Finzi, X. Wu, C. Dogo-Isonagie, L. K. Lee, L. R. Moore, S. D. Schmidt, J. Stuckey, Y. Yang, T. Zhou, J. Zhu, D. A. Vicic, A. K. Debnath, L. Shapiro, C. A. Bewley, J. R. Mascola, J. G. Sodroski, P. D. Kwong
Unliganded Hiv-1 Gp120 Core Structures Assume The Cd4-Bound Conformation With Regulation By Quaternary Interactions And Variable Loops.
Proc. Natl. Acad. Sci. Usa V. 109 5663 2012
PubMed-ID: 22451932  |  Reference-DOI: 10.1073/PNAS.1112391109

(-) Compounds

Molecule 1 - HIV-1 CLADE C ZM109F.PB4 GP120
    Chains: A, B, C, D
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293
    Expression System Plasmid: PVRC8400
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: HIV-1 ENV
    Organism Common: HIV-1
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3TIH)

(-) Sites  (0, 0)

(no "Site" information available for 3TIH)

(-) SS Bonds  (30, 30)

Asymmetric Unit
No.Residues
1A:54 -A:74
2A:119 -A:205
3A:218 -A:247
4A:228 -A:239
5A:296 -A:331
6A:378 -A:445
7A:385 -A:418
8B:54 -B:74
9B:119 -B:205
10B:218 -B:247
11B:228 -B:239
12B:296 -B:331
13B:378 -B:445
14B:385 -B:418
15C:54 -C:74
16C:119 -C:205
17C:218 -C:247
18C:228 -C:239
19C:296 -C:331
20C:331 -C:385
21C:331 -C:418
22C:378 -C:445
23C:385 -C:418
24D:54 -D:74
25D:119 -D:205
26D:218 -D:247
27D:228 -D:239
28D:296 -D:331
29D:378 -D:445
30D:385 -D:418

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3TIH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TIH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TIH)

(-) Exons   (0, 0)

(no "Exon" information available for 3TIH)

(-) 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:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eee.........hhhhhh...ee........ee.....eeee....hhhhhhhhhhhhhhh......eee....ee..............eee....eeeeee.......eeee..eeee.............eee..........eee.........eeeeeeeeeeeeee.........eeeee.hhhh.....hhhhhh..eeee......hhhhhheeeee..eeeee..hhhhh...eeeee....eee......eee..........eeeeeeeeee......eeee......hhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tih A  44 VWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIECIRPGNGDIRKAYCKINGSEWNETLTKVSEKLKKTIRFAQHSGGDLEVTTHSFNCRGEFFYCNTSELFNSSNITLPCRIKQIINMWQGVGRAMYAPPIRGEIKCTSNITGILLTRDGSTEEIFRPEGGNMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348 ||    364       374       384       412       422       432       442       452     ||466       476       486      
                                                                                                          124|                                                                                                    301|                       350|                                 393|                                           458|                             
                                                                                                           198                                                                                                     324                        357                                  412                                            463                             


Chain B from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eee.........hhhhhh...ee........ee.....eeee....hhhhhhhhhhhhhhh......eee....ee..............eee....eeeeee.......eeee..eeee.............eee..........eee.........eeeeeeeeeeeeee.........eeeee.hhhh.....hhhhhh..eeee......hhhhhheeeee..eeeee..hhhhh...eeeee....eee......eee..........eeeeeeeeee......eeee......hhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tih B  44 VWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIECIRPGNGDIRKAYCKINGSEWNETLTKVSEKLKKTIRFAQHSGGDLEVTTHSFNCRGEFFYCNTSELFNSSNITLPCRIKQIINMWQGVGRAMYAPPIRGEIKCTSNITGILLTRDGSTEEIFRPEGGNMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348 ||    364       374       384       412       422       432       442       452     ||466       476       486      
                                                                                                          124|                                                                                                    301|                       350|                                 393|                                           458|                             
                                                                                                           198                                                                                                     324                        357                                  412                                            463                             


Chain C from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eee.........hhhhhh...ee........ee.....eeee....hhhhhhhhhhhhhhh......eee....ee..............eee....eeeeee.......eeee..eeee.............eee..........eee.........eeeeeeeeeeeeee.........eeeee.hhhh.....hhhhhh..eeee......hhhhhheeeee..eeeee..hhhhh...eeeee....eee......eee..........eeeeeeeeee......eeee......hhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tih C  44 VWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIECIRPGNGDIRKAYCKINGSEWNETLTKVSEKLKKTIRFAQHSGGDLEVTTHSFNCRGEFFYCNTSELFNSSNITLPCRIKQIINMWQGVGRAMYAPPIRGEIKCTSNITGILLTRDGSTEEIFRPEGGNMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348 ||    364       374       384       412       422       432       442       452     ||466       476       486      
                                                                                                          124|                                                                                                    301|                       350|                                 393|                                           458|                             
                                                                                                           198                                                                                                     324                        357                                  412                                            463                             


Chain D from PDB  Type:PROTEIN  Length:326
                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee......eee.........hhhhhh...ee........ee.....eeee....hhhhhhhhhhhhhhh......eee....ee..............eee....eeeeee.......eeee..eeee.............eee..........eee.........eeeeeeeeeeeeee.........eeeee.hhhh.....hhhhhh..eeee......hhhhhheeeee..eeeee..hhhhh...eeeee....eee......eee..........eeeeeeeeee......eeee......hhhhhhh......eeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tih D  44 VWKEAKTTLFCASDAKSYEREVHNVWATHACVPTDPDPQELVMANVTENFNMWKNDMVDQMHEDIISLWDQSLKPCVKLTGGSTITQACPKVSFDPIPIHYCAPAGYAILKCNNKTFSGKGPCSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIRSENLTDNAKTIIVHLNKSVEIECIRPGNGDIRKAYCKINGSEWNETLTKVSEKLKKTIRFAQHSGGDLEVTTHSFNCRGEFFYCNTSELFNSSNITLPCRIKQIINMWQGVGRAMYAPPIRGEIKCTSNITGILLTRDGSTEEIFRPEGGNMRDNWRSELYKYKVVEIK 492
                                    53        63        73        83        93       103       113       123||     206       216       226       236       246       256       266       276       286       296    || 328       338       348 ||    364       374       384       412       422       432       442       452     ||466       476       486      
                                                                                                          124|                                                                                                    301|                       350|                                 393|                                           458|                             
                                                                                                           198                                                                                                     324                        357                                  412                                            463
   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)

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(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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3tgq 3tgr 3tgs 3tgt