Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-HIV LLAMA VHH ANTIBODY A12 IN COMPLEX WITH C186 GP120
 
Authors :  L. Chen, J. S. Mclellan, Y. D. Kwon, S. Schmidt, X. Wu, T. Zhou, Y. Yang, B. A. Forsman, R. A. Weiss, T. Verrips, J. Mascola, P. D. Kwong
Date :  15 Apr 11  (Deposition) - 02 May 12  (Release) - 12 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ig Vh Domain, Anti-Hiv, Viral Protein-Immune System Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, J. S. Mclellan, Y. D. Kwon, S. Schmidt, X. Wu, T. Zhou, Y. Yang, B. Zhang, A. Forsman, R. A. Weiss, T. Verrips, J. Mascola, P. D. Kwong
Crystal Structure Of Anti-Hiv A12 Vhh Of Llama Antibody In Complex With C1086 Gp120
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - C186 GP120
    Chains: A
    Engineered: YES
    Organism Scientific: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
    Organism Taxid: 11706
 
Molecule 2 - LLAMA VHH A12
    Chains: B
    Engineered: YES
    Organism Scientific: LAMA GLAMA
    Organism Taxid: 9844

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1NAG8Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:234 , THR A:236 , PRO A:238 , ILE A:272BINDING SITE FOR RESIDUE NAG A 734
2AC2SOFTWAREASN A:229 , ASN A:241 , SER A:243BINDING SITE FOR RESIDUE NAG A 741
3AC3SOFTWAREASP A:211 , LYS A:252 , VAL A:254 , ASN A:262 , ASN A:446 , SER A:447BINDING SITE FOR RESIDUE NAG A 762
4AC4SOFTWAREASN A:276 , THR A:278BINDING SITE FOR RESIDUE NAG A 776
5AC5SOFTWAREGLU A:268 , GLU A:269 , ILE A:270 , ASN A:289 , GLU A:290 , GLU A:348BINDING SITE FOR RESIDUE NAG A 789
6AC6SOFTWAREASN A:386 , SER A:388BINDING SITE FOR RESIDUE NAG A 886
7AC7SOFTWAREASP A:389 , ASN A:392 , THR A:403 , GLY A:404BINDING SITE FOR RESIDUE NAG A 892
8AC8SOFTWAREPRO A:81 , CYS A:247 , THR A:248 , HIS A:249 , ASN A:397BINDING SITE FOR RESIDUE NAG A 897

(-) SS Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1A:54 -A:74
2A:218 -A:247
3A:228 -A:239
4A:296 -A:331
5A:378 -A:445
6A:385 -A:418
7B:22 -B:92

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:81 -Gln A:82

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3RJQ)

(-) Sequences/Alignments

Asymmetric/Biological 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:292
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.....eeee.......hhhhhhhhhhhee.......ee.....eeee...hhhhhhhhhhhhhhhhhhh.........eee....eeeeee.......eeee..eeee.............eee.........eee..........eeeeeeeeeeeee...eeeehhhhhhhhhhhhhhhhhhhh....ee.......hhhhhheeeee..eeeee.......eee....ee....eeeeee....eeeeeeeeeeee......eee....hhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                3rjq A   45 WKEAKTTLFCASDAKAYEKEVHNVWATHACVPTDPNPQEMVLANVTENFNMWKNDMVEQMHEDIISLWDESLKVSFDPIPLHYCAPAGFAILKCNNKTFNGTGPCRNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIIIRSENLTNNAKTIIVHLNESVNIVCTRAHCNINESKWNNTLQKVGEELAKHFPSKTIKFEPSSGGDLEITTHSFNCRGEFFYCNTSDLFNGTYRNGTYNHTGTITLQCKIKQTCNSNITGLLLLRDGDTETFRPGGGDMRDNWRSELYKYKVVEI  491
                                    54        64        74        84        94       104       114  ||   214       224       234       244       254       264       274       284       294   ||  334       344       354|      365       375       385       395       413       444       454   ||  469       479       489  
                                                                                                  117|                                                                                       298|                      354|                                             404|      422|           458|                           
                                                                                                   208                                                                                        329                       356                                              413       444            464                           


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                                
               SCOP domains d3rjqb_ B: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee....eeeeeee.......eeeeeeee.....eeeeeeee.....eee.......eeeeee....eeeeee...hhhhheeeeeeeee...............ee...eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                3rjq B    1 AVQLQESGGGLVQAGGSLRLSCTASGRISSSYDMGWFRQAPGKEREFVAAISWSGGTTDYADSVKGRFAISKDNAKNAVYLQMNSLKPEDTAVYYCAAKWRPLRYSDYPSNSDYYDWGQGTQVTVSS  113
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F||||   106       
                                                                              52A                            82A||               100A|||||100J             
                                                                                                              82B|                100B|||||||              
                                                                                                               82C                 100C||||||              
                                                                                                                                    100D|||||              
                                                                                                                                     100E||||              
                                                                                                                                      100F|||              
                                                                                                                                       100G||              
                                                                                                                                        100H|              
                                                                                                                                         100I
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RJQ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3RJQ)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:81 - Gln A:82   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3rjq
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProt
 
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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3RJQ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RJQ)