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(-) Description

Title :  ANTIBODY FAB FRAGMENT 447-52D IN COMPLEX WITH UG1033 PEPTIDE
 
Authors :  A. K. Dhillon, R. L. Stanfield, I. A. Wilson
Date :  24 Jan 08  (Deposition) - 08 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Keywords :  Antibody Fab Hiv-1 Peptide, Envelope Protein, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Dhillon, R. L. Stanfield, M. K. Gorny, C. Williams, S. Zolla-Pazner, I. A. Wilson
Structure Determination Of An Anti-Hiv-1 Fab 447-52D-Peptide Complex From An Epitaxially Twinned Data Set
Acta Crystallogr. , Sect. D V. 64 792 2008
PubMed-ID: 18566514  |  Reference-DOI: 10.1107/S0907444908013978
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LAMBDA-CHAIN
    ChainsL, M
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
 
Molecule 2 - FAB 447-52D, HEAVY CHAIN
    ChainsH, I
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
 
Molecule 3 - ENVELOPE GLYCOPROTEIN
    ChainsP, Q
    EngineeredYES
    Other DetailsTHE PEPTIDE IS NATURALLY FOUND IN HIV-1 GP120.
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit HILMPQ
Biological Unit 1 (1x)H L P 
Biological Unit 2 (1x) I M Q

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3C2A)

(-) Sites  (0, 0)

(no "Site" information available for 3C2A)

(-) SS Bonds  (10, 10)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3I:22 -I:92
4I:142 -I:208
5L:23 -L:88
6L:134 -L:194
7L:214 -H:127
8M:23 -M:88
9M:134 -M:194
10M:214 -I:127

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:148 -Pro H:149
3Glu H:150 -Pro H:151
4Tyr M:140 -Pro M:141
5Phe I:148 -Pro I:149
6Glu I:150 -Pro I:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C2A)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGLC2_HUMAN85-91
 
  2L:192-198
M:192-198
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGLC2_HUMAN85-91
 
  1L:192-198
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IG_MHCPS00290 Immunoglobulins and major histocompatibility complex proteins signature.IGLC2_HUMAN85-91
 
  1-
M:192-198

(-) Exons   (1, 2)

Asymmetric Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003903231ENSE00001721671chr22:23243156-23243617462IGLC2_HUMAN1-1061062L:107-214 (gaps)
M:107-214 (gaps)
108
108

(-) 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 H from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                        
               SCOP domains d3c2ah1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                     d3c2ah2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 3c2aH01 H:1-113 Immunoglobulins                                                                                                    3c2aH02 H:114-223 Immunoglobulins                                                                 -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhhh..eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee....eeeeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3c2a H    1 EVQLVESGGGLVKPGGSLRLTCVASGFTFSDVWLNWVRQAPGKGLEWVGRIKSRTDGGTTDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCTTDGFIMIRGVSEDYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEL  227
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122       134       144       154|||    169|      180|      191       203|      214       226 
                                                                              52A||                            82A||               100A|||||100J||                           130|                  154|||    169|      180|               200||               223| 
                                                                               52B|                             82B|                100B|||||100K|                            133                   156||     171       182                203|                226 
                                                                                52C                              82C                 100C|||||100L                                                   157|                                   205                    
                                                                                                                                      100D|||||                                                       162                                                          
                                                                                                                                       100E||||                                                                                                                    
                                                                                                                                        100F|||                                                                                                                    
                                                                                                                                         100G||                                                                                                                    
                                                                                                                                          100H|                                                                                                                    
                                                                                                                                           100I                                                                                                                    

Chain I from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                        
               SCOP domains d3c2ai1 I:1-113 Immunoglobulin heavy chain variable domain, VH                                                                     d3c2ai2 I:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains 3c2aI01 I:1-113 Immunoglobulins                                                                                                    3c2aI02 I:114-223 Immunoglobulins                                                                 -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee........eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee....eeeeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3c2a I    1 EVQLVESGGGLVKPGGSLRLTCVASGFTFSDVWLNWVRQAPGKGLEWVGRIKSRTDGGTTDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCTTDGFIMIRGVSEDYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEL  227
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122       134       144       154|||    169|      180|      191       203|      214       226 
                                                                              52A||                            82A||               100A|||||100J||                           130|                  154|||    169|      180|               200||               223| 
                                                                               52B|                             82B|                100B|||||100K|                            133                   156||     171       182                203|                226 
                                                                                52C                              82C                 100C|||||100L                                                   157|                                   205                    
                                                                                                                                      100D|||||                                                       162                                                          
                                                                                                                                       100E||||                                                                                                                    
                                                                                                                                        100F|||                                                                                                                    
                                                                                                                                         100G||                                                                                                                    
                                                                                                                                          100H|                                                                                                                    
                                                                                                                                           100I                                                                                                                    

Chain L from PDB  Type:PROTEIN  Length:216
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:216
                                                                                                                                           1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79        89        99      
         IGLC2_HUMAN      - ---------------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  105
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -3c2aL01 L:2-107 Immunoglobulins                                                                                3c2aL02 L:108-211 Immunoglobulins                                                                    --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeeehhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
               Transcript 1 ---------------------------------------------------------------------------------------------------------------Exon 1.1  PDB: L:107-214 (gaps) UniProt: 1-106                                                            Transcript 1
                3c2a L    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  214
                                    11        21      ||29        39        49        59        69        79        89      ||96       106|      115       125       135       145       155       165  ||   176       186       196   ||  208      
                                    9|              27A|                                                                  95A||        106A                                                           168|                           200|           
                                    11               27B                                                                   95B|                                                                        170                            203           
                                                                                                                            95C                                                                                                                     

Chain M from PDB  Type:PROTEIN  Length:216
 aligned with IGLC2_HUMAN | P0DOY2 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:216
                                                                                                                                           1                                                                                                        
                                     -         -         -         -         -         -         -         -         -         -         - |       9        19        29        39        49        59        69        79        89        99      
         IGLC2_HUMAN      - ---------------------------------------------------------------------------------------------------------------GQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  105
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains -3c2aM01 M:2-107 Immunoglobulins                                                                                3c2aM02 M:108-211 Immunoglobulins                                                                    --- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeee......eeee.............eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee...ee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IG_MHC -------------- PROSITE
               Transcript 1 ---------------------------------------------------------------------------------------------------------------Exon 1.1  PDB: M:107-214 (gaps) UniProt: 1-106                                                            Transcript 1
                3c2a M    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  214
                                    11        21      ||29        39        49        59        69        79        89      ||96       106|      115       125       135       145       155       165  ||   176       186       196   ||  208      
                                    9|              27A|                                                                  95A||        106A                                                           168|                           200|           
                                    11               27B                                                                   95B|                                                                        170                            203           
                                                                                                                            95C                                                                                                                     

Chain P from PDB  Type:PROTEIN  Length:13
 aligned with Q9YWB6_9HIV1 | Q9YWB6 from UniProtKB/TrEMBL  Length:109

    Alignment length:13
                                    58   
        Q9YWB6_9HIV1     49 KSIHLGPGRAFYA   61
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eeee......ee Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                3c2a P  305 KSIHLGPGRAFYA  319
                                || 316   
                              309|       
                               312       

Chain Q from PDB  Type:PROTEIN  Length:13
 aligned with Q9YWB6_9HIV1 | Q9YWB6 from UniProtKB/TrEMBL  Length:109

    Alignment length:13
                                    58   
        Q9YWB6_9HIV1     49 KSIHLGPGRAFYA   61
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eeee........ Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                3c2a Q  305 KSIHLGPGRAFYA  319
                                || 316   
                              309|       
                               312       

   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  (2, 4)

Asymmetric Unit

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
1a3c2aH02H:114-223
1b3c2aI02I:114-223
1c3c2aL01L:2-107
1d3c2aM01M:2-107
1e3c2aL02L:108-211
1f3c2aM02M:108-211
1g3c2aH01H:1-113
1h3c2aI01I:1-113

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C2A)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain L,M   (IGLC2_HUMAN | P0DOY2)

Chain P,Q   (Q9YWB6_9HIV1 | Q9YWB6)
biological process
    GO:0039663    membrane fusion involved in viral entry into host cell    Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
    GO:0046718    viral entry into host cell    The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019062    virion attachment to host cell    The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0019031    viral envelope    The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
    GO:0019012    virion    The complete fully infectious extracellular virus particle.
    GO:0055036    virion membrane    The lipid bilayer surrounding a virion.

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    Glu H:150 - Pro H:151   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        IGLC2_HUMAN | P0DOY21jvk 1lil 1zvo 2jb5 2jb6 3tv3 3twc 3tyg 4eow 4lld 4llm 4llq 4llu 4llw 4lly 4o58 4o5i 5d9q 5iq7 5iq9

(-) Related Entries Specified in the PDB File

1q1j 447-52D IN COMPLEX WITH V3 PEPTIDE