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(-) Description

Title :  TRIPLE HELIX BUNDLE OF GP41 COMPLEXED WITH FAB 8066
 
Authors :  M. Li, Gustchina, A, A. Wlodawer
Date :  01 May 13  (Deposition) - 12 Mar 14  (Release) - 12 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.82
Chains :  Asym. Unit :  A,H,L
Biol. Unit 1:  A,H,L  (1x)
Biol. Unit 2:  A,H,L  (3x)
Keywords :  Gp41 Fab Immune System, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Gustchina, M. Li, R. Ghirlando, P. Schuck, J. M. Louis, J. Pierson, P. Rao, S. Subramaniam, A. Gustchina, G. M. Clore, A. Wlodawer
Complexes Of Neutralizing And Non-Neutralizing Affinity Matured Fabs With A Mimetic Of The Internal Trimeric Coiled-Coil Of Hiv-1 Gp41.
Plos One V. 8 78187 2013
PubMed-ID: 24244293  |  Reference-DOI: 10.1371/JOURNAL.PONE.0078187

(-) Compounds

Molecule 1 - GP41 HELIX
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
 
Molecule 2 - 8066 HEAVY CHAIN
    Chains: H
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - 8066 LIGHT CHAIN
    Chains: L
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : AHL
Biological Unit 1 (1x): AHL
Biological Unit 2 (3x): AHL

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4KHT)

(-) Sites  (0, 0)

(no "Site" information available for 4KHT)

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1A:2 -A:3
2H:22 -H:95
3H:147 -H:203
4L:22 -L:87
5L:136 -L:195

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ala H:121 -Ser H:122
2Phe H:153 -Pro H:154
3Glu H:155 -Pro H:156
4Gly L:24 -Asp L:25
5Pro L:28 -Tyr L:29
6Gly L:109 -Gln L:110
7Tyr L:142 -Pro L:143

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KHT)

(-) 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:66
                                                                                                  
               SCOP domains ------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                 4kht A   2 CCGGIKKEIEAIKKEQEAIKKKIEAIEKELSGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARIL  67
                                    11        21        31        41        51        61      


Chain H from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee...ee......eeeeeee...hhhhheeeeeee.....eeeeeee......eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........ee...eeee.........eeee.......eeeeeeeeee.....eeee.hhh....eeeeeeee.....eeeeeeeee...........eeeeehhhheee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kht H   3 QLVQSGAEVKKPGSSVKVSCKASGGTFNSYAFSWVRQAPGQGLEWMGSIIPIFGTTNYAQKFQGRVTITADESTSTAYMELSSLRSEDTAVYYCARYFDTYNNYGFANWGQGTLVTVSSASTKGPSVFPLAPSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP 220
                                    12        22        32        42        52|       61        71        81        91       101       111       121       131  ||   146       156       166       176       186       196       206       216    
                                                                            52A                                                                               134|                                                                                
                                                                                                                                                               140                                                                                


Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains d4khtl1 L:2-109 automated matches                                                                           d4khtl2 L:110-210 automated matches                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee......eeeeee.........eeeee......eeeee............eeeeee..eeeeee.........eeeeeee......eee...eeee............ee..hhhhhhh....eee..eee.....eeeeee..ee.....ee..........ee..eee............eeeeee....ee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kht L   2 IELTQPPSVSVVPGQTARISCSGDNIPYEYASWYQQKPGQAPVLVIYGDNNRPSGIPERFSGSNSGNTATLTISGTQAEDEADYYCASWDSMTVDGVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP 210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201
   Legend:   → Mismatch (orange background)
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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 Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4kht)
 
  Cis Peptide Bonds
    Ala H:121 - Ser H:122   [ RasMol ]  
    Glu H:155 - Pro H:156   [ RasMol ]  
    Gly L:109 - Gln L:110   [ RasMol ]  
    Gly L:24 - Asp L:25   [ RasMol ]  
    Phe H:153 - Pro H:154   [ RasMol ]  
    Pro L:28 - Tyr L:29   [ RasMol ]  
    Tyr L:142 - Pro L:143   [ RasMol ]  
 
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  A1YNW7_9HIV1 | A1YNW7
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 Related Entries

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

UniProtKB/Swiss-Prot
        A1YNW7_9HIV1 | A1YNW7: 5hfl
UniProtKB/TrEMBL
        A1YNW7_9HIV1 | A1YNW7: 4khx

(-) Related Entries Specified in the PDB File

3ma9 DIFFERENT HELIX BUNDLE
4khx