Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE STABILIZED INNER DOMAIN OF CLADE A/E HIV-1 GP120 FROM E. COLI IN COMPLEX WITH THE ANTIBODY A32.
 
Authors :  W. D. Tolbert, N. Gohain, M. Pazgier
Date :  19 Feb 15  (Deposition) - 02 Mar 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.02
Chains :  Asym. Unit :  A,B,C,G,H,L
Biol. Unit 1:  G,H,L  (1x)
Biol. Unit 2:  A,B,C  (1x)
Keywords :  Adcc, Non-Neutralizing, Anti-Hiv-1 Env Antibody A32, Cd4I Antibody, Clade A/E 93Th057, Viral Protein, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, M. L. Visciano, M. Ebadi, A. L. Devico, T. R. Fouts, A. Finzi, G. K. Lewis M. Pazgier
Paring Down Hiv Env: Design And Crystal Structure Of A Stabilized Inner Domain Of Hiv-1 Gp120 Displaying A Major Adcc Target Of The A32 Region.
Structure V. 24 697 2016
PubMed-ID: 27041594  |  Reference-DOI: 10.1016/J.STR.2016.03.005

(-) Compounds

Molecule 1 - THE STABILIZED INNER DOMAIN OF CLADE A/E HIV-1 GP120 FROM E. COLI
    Chains: G, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ORIGAMI(DE)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS 1
    Organism Taxid: 11676
    Variant: CLADE A/E
 
Molecule 2 - THE ANTIBODY A32 FAB HEAVY CHAIN.
    Chains: H, B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - THE ANTIBODY A32 FAB LIGHT CHAIN.
    Chains: L, C
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK 293 CELLS
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCGHL
Biological Unit 1 (1x):    GHL
Biological Unit 2 (1x): ABC   

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4YC2)

(-) Sites  (0, 0)

(no "Site" information available for 4YC2)

(-) SS Bonds  (16, 16)

Asymmetric Unit
No.Residues
1A:54 -A:74
2A:65 -A:115
3A:218 -A:247
4A:228 -A:239
5B:22 -B:92
6B:140 -B:196
7C:23 -C:88
8C:134 -C:193
9G:54 -G:74
10G:65 -G:115
11G:218 -G:247
12G:228 -G:239
13H:22 -H:92
14H:140 -H:196
15L:23 -L:88
16L:134 -L:193

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Gly H:26 -Gly H:27
2Lys H:43 -Gly H:44
3Phe H:146 -Pro H:147
4Glu H:148 -Pro H:149
5Tyr L:140 -Pro L:141
6Tyr B:40 -Pro B:41
7Lys B:43 -Gly B:44
8Phe B:146 -Pro B:147
9Glu B:148 -Pro B:149
10Tyr C:140 -Pro C:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YC2)

(-) Exons   (0, 0)

(no "Exon" information available for 4YC2)

(-) 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:131
                                                                                                                                                                    
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee.......hhhhhhhhh..ee.....................hhhhhhhhhhhhhhhhhhh......eee....eeeee.........................hhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yc2 A   45 WKDADTTLFCASDAKAHETECHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQCLFDPIPIHYCTPAGYVILKCNDFNGTGPCKNVSSVQCTHGIKPIKDNWRSELYKYKVVQI  491
                                    54        64        74        84        94       104       114 ||    217       227  ||   239       249   ||  480       490 
                                                                                                 116|                 230|                 253|                
                                                                                                  210                  233                  475                


Chain B from PDB  Type:PROTEIN  Length:223
                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee.......eeeeeeee.....eeeeeeee....eee.......eeeeee....eeeeeee..hhhhheeeeeeeee.......eeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yc2 B    1 QVQLQESGPGLVKPSQTLSLSCTVSGSSSSGAHYWSWIRQYPGKGLEWIGYIHYSGNTYYNPSLKSRITISQHTSENQFSLKLNSVTVADTAVYYCARGTRLRTLRNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20     || 31    ||  39        49        59        69        79   |||  86        96    |||101       111       121       131       141       151       161       171       181       191       201       211   
                                                    26|     35A|                                             82A||               100A||||                                                                                                                  
                                                     28      35B                                              82B|                100B|||                                                                                                                  
                                                                                                               82C                 100C||                                                                                                                  
                                                                                                                                    100D|                                                                                                                  
                                                                                                                                     100E                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....eeeeeee...........eeeeee......eeee.............eeeee...eeeeeee..hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhhh...eeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeee.hhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4yc2 C    4 VLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQHHPGKAPKLIISEVNNRPSGVPDRFSGSKSGNTASLTVSGLQAEDEAEYYCSSYTDIHNFVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    13        23    ||| 30        40        50        60        70        80        90     |  99       108       118       128       138       148       158       168       178       188       198       208
                                                  27A||                                                                  95A        106A                                                                                                      
                                                   27B|                                                                                                                                                                                       
                                                    27C                                                                                                                                                                                       


Chain G from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee.......hhhhhhhhh..ee......eee.....eeee.hhh....hhhhhhhhhhhhhh.....eeee....eeeeee.......eeee..eeee.........hhhhhhhhh.eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yc2 G   45 WKDADTTLFCASDAKAHETECHNVWATHACVPTDPNPQEIHLENVTENFNMWKNNMVEQMQEDVISLWDQCLFDPIPIHYCTPAGYVILKCNDKNFNGTGPCKNVSSVQCTHGIKPIKDNWRSELYKYKVVQI  491
                                    54        64        74        84        94       104       114 ||    217       227       237       247     ||478       488   
                                                                                                 116|                                        253|                
                                                                                                  210                                         475                


Chain H from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                             
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee....eeeeeeeee..hhhhh.eeeeeeee......eeeeeee....eee.......eeeeee....eeeeeee..hhhhheeeeeeeee.......eeeee...eeeee........eeeee.......eeeeeeeeee........hhhhh....eee..........eeeeeeeeehhhhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yc2 H    1 QVQLQESGPGLVKPSQTLSLSCTVSGGSSSSGAHYWSWIRQYPGKGLEWIGYIHYSGNTYYNPSLKSRITISQHTSENQFSLKLNSVTVADTAVYYCARGTRLRTLRNAFDIWGQGTMVTVSSASTKGPSVFPLAPSSKGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPK  214
                                    10        20        30     || 38        48        58        68        78    ||| 85        95     |100E       110       120       134       144       154       164       174       184       194       204       214
                                                             35A|                                             82A||               100A||||                          129|                                                                                
                                                              35B                                              82B|                100B|||                           134                                                                                
                                                                                                                82C                 100C||                                                                                                              
                                                                                                                                     100D|                                                                                                              
                                                                                                                                      100E                                                                                                              


Chain L from PDB  Type:PROTEIN  Length:210
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee....eeeeeee............eeeee......eeee.............eeeee...eeeeeee..hhhhheeeeeeee.....eee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4yc2 L    4 VLTQPPSASGSPGQSVTISCTGTSSDVGGYNYVSWYQHHPGKAPKLIISEVNNRPSGVPDRFSGSKSGNTASLTVSGLQAEDEAEYYCSSYTDIHNFVFGGGTKLTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAP  208
                                    13        23    ||| 30        40        50        60        70        80        90     |  99       108       118       128       138       148       158       168       178       188       198       208
                                                  27A||                                                                  95A        106A                                                                                                      
                                                   27B|                                                                                                                                                                                       
                                                    27C
   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  (0, 0)

(no "SCOP Domain" information available for 4YC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YC2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YC2)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4yc2)
 
  Sites
(no "Sites" information available for 4yc2)
 
  Cis Peptide Bonds
    Glu B:148 - Pro B:149   [ RasMol ]  
    Glu H:148 - Pro H:149   [ RasMol ]  
    Gly H:26 - Gly H:27   [ RasMol ]  
    Lys B:43 - Gly B:44   [ RasMol ]  
    Lys H:43 - Gly H:44   [ RasMol ]  
    Phe B:146 - Pro B:147   [ RasMol ]  
    Phe H:146 - Pro H:147   [ RasMol ]  
    Tyr B:40 - Pro B:41   [ RasMol ]  
    Tyr C:140 - Pro C:141   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4yc2
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  A0A0M3KKW9_9 | A0A0M3KKW9
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  A0A0M3KKW9_9 | A0A0M3KKW9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0M3KKW9_9 | A0A0M3KKW9: 4s1q 4s1r 4s1s 4ybl 5cd5 5f96 5f9o 5f9w 5fcu 5kjr 5te6 5u6e

(-) Related Entries Specified in the PDB File

3tnm A32 FAB STRUCTURE.
4h8w CRYSTAL STRUCTURE OF THE CLADE A/E HIV-1 GP120 CORE IN COMPLEX WITH THE ANTIBODY N5-I5.
4rqh CRYSTAL STRUCTURE OF THE CLADE A/E HIV-1 GP120 INNER DOMAIN IN COMPLEX WITH THE ANTIBODY JR4.
4ybl CRYSTAL STRUCTURE OF THE CLADE A/E HIV-1 GP120 STABILIZED INNER DOMAIN IN COMPLEX WITH THE ANTIBODY A32.