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(-) Description

Title :  CRYSTAL STRUCTURE OF ANTI-HIV-1 FAB 447-52D IN COMPLEX WITH V3 CYCLIC PEPTIDE MN
 
Authors :  A. Killikelly, X. P. Kong
Date :  02 Aug 13  (Deposition) - 04 Sep 13  (Release) - 25 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  H,I,L,M,P,Q
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  I,M,Q  (1x)
Keywords :  Hiv, V3 Loop, Antibody-Antigen Interactions, Envelope, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Killikelly, H. T. Zhang, B. Spurrier, C. Williams, M. K. Gorny, S. Zolla-Pazner, X. P. Kong
Thermodynamic Signatures Of The Antigen Binding Site Of Mab 447-52D Targeting The Third Variable Region Of Hiv-1 Gp120.
Biochemistry V. 52 6249 2013
PubMed-ID: 23944979  |  Reference-DOI: 10.1021/BI400645E

(-) Compounds

Molecule 1 - FAB MAB 447-52D LIGHT CHAIN
    Chains: L, M
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB MAB 447-52D HEAVY CHAIN
    Chains: H, I
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Taxid: 9606
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 3 - CYCLIC V3 ARCH PEPTIDE
    Chains: P, Q
    Engineered: YES
    Synthetic: YES

 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  (1, 17)

Asymmetric Unit (1, 17)
No.NameCountTypeFull Name
1GOL17Ligand/IonGLYCEROL
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO L:59 , ARG L:61 , GLN L:79 , GOL L:304 , HOH L:551 , HOH L:596 , HOH L:604BINDING SITE FOR RESIDUE GOL L 301
02AC2SOFTWAREGLN H:39 , LEU H:45 , SER H:91 , TRP H:103 , GLY H:104 , GOL H:301 , HOH H:425 , GLN L:38 , HOH L:601BINDING SITE FOR RESIDUE GOL L 302
03AC3SOFTWAREVAL L:19 , THR L:20 , HOH L:493 , HOH L:598 , PHE P:317BINDING SITE FOR RESIDUE GOL L 303
04AC4SOFTWAREGLN L:37 , LYS L:45 , ASP L:82 , GOL L:301 , HOH L:630 , HOH L:656BINDING SITE FOR RESIDUE GOL L 304
05AC5SOFTWARESER L:26 , SER L:27 , HOH L:448 , HOH L:571 , HOH L:575 , HOH L:673BINDING SITE FOR RESIDUE GOL L 305
06AC6SOFTWAREGLY L:29 , ASN L:30 , ASN L:31 , TYR L:32 , ASN L:51 , LYS L:66 , HOH L:597 , HOH L:642BINDING SITE FOR RESIDUE GOL L 306
07AC7SOFTWAREGLN H:39 , GLY H:44 , LEU H:45 , HOH H:602 , GLY L:99 , GLY L:100 , GLY L:101 , GOL L:302 , HOH L:663BINDING SITE FOR RESIDUE GOL H 301
08AC8SOFTWAREPHE H:27 , THR H:28 , HOH H:447 , HOH H:496 , ASN M:30 , ASN M:31 , TYR M:32 , ASN M:51 , LYS M:66BINDING SITE FOR RESIDUE GOL H 302
09AC9SOFTWARELYS H:52 , ASP H:58 , SER L:65 , THR L:72 , LEU L:95 , HOH L:413 , GLY P:314 , HOH P:407BINDING SITE FOR RESIDUE GOL H 303
10BC1SOFTWAREARG H:52B , GLY H:55 , ARG H:71 , ASP H:73 , HOH H:410 , HOH H:638 , HOH H:686 , PRO L:109 , HOH L:499BINDING SITE FOR RESIDUE GOL H 304
11BC2SOFTWAREPHE H:97 , TYR H:100J , HOH H:534 , HOH H:666 , HOH H:698 , ASN M:30 , ARG P:306BINDING SITE FOR RESIDUE GOL H 305
12BC3SOFTWAREASP H:101 , VAL H:102 , TRP H:103 , HOH H:462 , GLU I:100E , ALA L:43 , PRO L:44 , PHE Q:317 , TYR Q:318BINDING SITE FOR RESIDUE GOL H 306
13BC4SOFTWAREALA I:61 , ASP M:95C , HOH M:429 , HOH M:438 , HOH M:456BINDING SITE FOR RESIDUE GOL M 301
14BC5SOFTWAREARG H:100A , ASP H:100F , SER M:26 , SER M:27 , SER M:27A , HOH M:536BINDING SITE FOR RESIDUE GOL M 302
15BC6SOFTWAREPRO M:59 , ARG M:61 , GLN M:79BINDING SITE FOR RESIDUE GOL M 303
16BC7SOFTWAREGLN I:39 , GLY I:44 , LEU I:45 , PHE M:87 , GLY M:99 , GLY M:100BINDING SITE FOR RESIDUE GOL I 301
17BC8SOFTWARELYS I:105 , THR I:107 , THR I:108 , HOH I:473 , HOH I:558BINDING SITE FOR RESIDUE GOL I 302

(-) SS Bonds  (11, 11)

Asymmetric Unit
No.Residues
1H:22 -H:92
2H:140 -H:196
3I:22 -I:92
4I:140 -I:196
5L:23 -L:88
6L:134 -L:193
7L:211 -H:127
8M:23 -M:88
9M:134 -M:193
10P:305 -P:320
11Q:305 -Q:320

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Tyr L:140 -Pro L:141
2Phe H:146 -Pro H:147
3Glu H:148 -Pro H:149
4Tyr M:140 -Pro M:141
5Phe I:146 -Pro I:147
6Glu I:148 -Pro I:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M1D)

(-) Exons   (0, 0)

(no "Exon" information available for 4M1D)

(-) 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 d4m1dh1 H:1-113 Immunoglobulin heavy chain variable domain, VH                                                                     d4m1dh2 H:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhhh..eee.hhhh..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
                4m1d H    1 EVQLVESGGGLVKPGGSLRLTCVASGFTFSDVWLNWVRQAPGKGLEWVGRIKSRTDGGTTDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCTTDGFIMIRGVSEDYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEL  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122       132       142       152       162       172       182       192       202       212 
                                                                              52A||                            82A||               100A|||||100J||                                                                                                                 
                                                                               52B|                             82B|                100B|||||100K|                                                                                                                 
                                                                                52C                              82C                 100C|||||100L                                                                                                                 
                                                                                                                                      100D|||||                                                                                                                    
                                                                                                                                       100E||||                                                                                                                    
                                                                                                                                        100F|||                                                                                                                    
                                                                                                                                         100G||                                                                                                                    
                                                                                                                                          100H|                                                                                                                    
                                                                                                                                           100I                                                                                                                    


Chain I from PDB  Type:PROTEIN  Length:231
                                                                                                                                                                                                                                                                        
               SCOP domains d4m1di1 I:1-113 Immunoglobulin heavy chain variable domain, VH                                                                     d4m1di2 I:114-213 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee........eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeeeeee....eeeeeeeeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.........eeeeeehhh.eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m1d I    1 EVQLVESGGGLVKPGGSLRLTCVASGFTFSDVWLNWVRQAPGKGLEWVGRIKSRTDGGTTDYAASVKGRFTISRDDSKNTLYLQMNSLKTEDTAVYSCTTDGFIMIRGVSEDYYYYYMDVWGKGTTVTVSSASTKGPSVFPLAPCSRSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYTCNVNHKPSNTKVDKRVEL  213
                                    10        20        30        40        50  |||   57        67        77     |||84        94      100D|||||||102       112       122       132       142       152       162       172       182       192       202       212 
                                                                              52A||                            82A||               100A|||||100J||                                                                                                                 
                                                                               52B|                             82B|                100B|||||100K|                                                                                                                 
                                                                                52C                              82C                 100C|||||100L                                                                                                                 
                                                                                                                                      100D|||||                                                                                                                    
                                                                                                                                       100E||||                                                                                                                    
                                                                                                                                        100F|||                                                                                                                    
                                                                                                                                         100G||                                                                                                                    
                                                                                                                                          100H|                                                                                                                    
                                                                                                                                           100I                                                                                                                    


Chain L from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                         
               SCOP domains d4m1dl1 L:1-106A automated matches                                                                             d4m1dl2 L:107-211 automated matches                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4m1d L    1 QSVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTEC  211
                                    11        21      ||29        39        49        59        69        79        89      ||96       106|      115       125       135       145       155       165       175       185       195       205      
                                    9|              27A|                                                                  95A||        106A                                                                                                         
                                    11               27B                                                                   95B|                                                                                                                     
                                                                                                                            95C                                                                                                                     


Chain M from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                      
               SCOP domains d4m1dm1 M:2-106A automated matches                                                                            d4m1dm2 M:107-209 automated matches                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4m1d M    2 SVLTQPPSVSAAPGQKVTISCSGSSSNIGNNYVLWYQQFPGTAPKLLIYGNNKRPSGIPDRFSGSKSGTSATLGITGLQTGDEADYFCATWDSGLSADWVFGGGTKLTVLSQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT  209
                                   |12        22     || 30        40        50        60        70        80        90     |||97      106A       116       126       136       146       156       166       176       186       196       206   
                                   9|              27A|                                                                  95A||        106A                                                                                                       
                                   11               27B                                                                   95B|                                                                                                                   
                                                                                                                           95C                                                                                                                   


Chain P from PDB  Type:PROTEIN  Length:14
                                               
               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
                4m1d P  305 CRIHIGPGRAFYTC  320
                                || 316    
                              309|        
                               312        


Chain Q from PDB  Type:PROTEIN  Length:14
                                               
               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
                4m1d Q  305 CRIHIGPGRAFYTC  320
                                || 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  (3, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M1D)

(-) Gene Ontology  (22, 22)

Asymmetric Unit(hide GO term definitions)

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  ENV_HV1MN | P05877
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 Related Entries

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

UniProtKB/Swiss-Prot
        ENV_HV1MN | P05877: 1acy 1ai1 1f58 1ggi 1k5m 1nak 1niz 1nj0 1q1j 2b0s 2qsc 3e6h 3go1 3mlw 3mlx 3uji 4xaw 4xbe 4xc1 4xc3 4xcf 4xmk
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(-) Related Entries Specified in the PDB File

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