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(-) Description

Title :  FAB 2G12 + MAN8
 
Authors :  D. A. Calarese, H. -K. Lee, M. D. Best, R. D. Astronomo, R. L. Stanfield, D. R. Burton, C. H. Wong, I. A. Wilson
Date :  09 May 05  (Deposition) - 09 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  H,K,L,M
Keywords :  Hiv Neutralizing Antibody; Anti-Carbohydrate; Domain- Swapping, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. A. Calarese, H. -K. Lee, C. Y. Huang, M. D. Best, R. D. Astronomo, R. L. Stanfield, H. Katinger, D. R. Burton, C. H. Wong, I. A. Wilson
Dissection Of The Carbohydrate Specificity Of The Broadly Neutralizing Anti-Hiv-1 Antibody 2G12
Proc. Natl. Acad. Sci. Usa V. 102 13372 2005
PubMed-ID: 16174734  |  Reference-DOI: 10.1073/PNAS.0505763102
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FAB 2G12, LIGHT CHAIN
    Chains: L, K
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell: DHFR
    Expression System Common: CHINESE HAMSTER
    Expression System Organ: OVARY
    Expression System Taxid: 10029
    Fragment: FAB, LIGHT CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - FAB 2G12, HEAVY CHAIN
    Chains: H, M
    Engineered: YES
    Expression System: CRICETULUS GRISEUS
    Expression System Cell: DHFR
    Expression System Common: CHINESE HAMSTER
    Expression System Organ: OVARY
    Expression System Taxid: 10029
    Fragment: FAB, HEAVY CHAIN
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : HKLM

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR H:55 , TYR L:94 , ASP M:100B , MAN M:230 , BMA M:233BINDING SITE FOR RESIDUE MAN M 229
2AC2SOFTWARETYR K:94 , ASP M:100B , MAN M:229 , MAN M:231BINDING SITE FOR RESIDUE MAN M 230
3AC3SOFTWAREALA M:31 , LEU M:100 , SER M:100A , ASP M:100B , MAN M:230 , MAN M:232BINDING SITE FOR RESIDUE MAN M 231
4AC4SOFTWAREGLY K:93 , ALA M:31 , HIS M:32 , THR M:33 , LYS M:95 , GLY M:96 , SER M:100A , ASP M:100B , ASN M:100C , ASP M:100D , MAN M:231BINDING SITE FOR RESIDUE MAN M 232
5AC5SOFTWARETHR H:52A , ASP M:100B , MAN M:229 , MAN M:234 , BMA M:235BINDING SITE FOR RESIDUE BMA M 233
6AC6SOFTWAREALA H:31 , THR H:52A , SER H:100A , BMA M:233 , MAN M:236BINDING SITE FOR RESIDUE MAN M 234
7AC7SOFTWARESER H:53 , BMA M:233BINDING SITE FOR RESIDUE BMA M 235
8AC8SOFTWAREALA H:31 , HIS H:32 , THR H:33 , LYS H:95 , GLY H:96 , SER H:100A , ASP H:100B , ASN H:100C , ASP H:100D , GLY L:93 , MAN M:234BINDING SITE FOR RESIDUE MAN M 236

(-) SS Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:92
2H:142 -H:208
3K:23 -K:88
4K:134 -K:194
5L:23 -L:88
6L:134 -L:194
7M:22 -M:92
8M:142 -M:208

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Ser L:7 -Pro L:8
2Tyr L:140 -Pro L:141
3Phe H:148 -Pro H:149
4Glu H:150 -Pro H:151
5Ser K:7 -Pro K:8
6Tyr K:140 -Pro K:141
7Phe M:148 -Pro M:149
8Glu M:150 -Pro M:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZLW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1ZLW)

(-) Exons   (0, 0)

(no "Exon" information available for 1ZLW)

(-) 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 H from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains d1zlwh1 H:1-112 Immunoglobulin heavy chain variable domain, VH                                                            -d1zlwh2 H:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                     - SCOP domains
               CATH domains 1zlwH01 H:1-113 Immunoglobulins                                                                                            1zlwH02 H:114-228 Immunoglobulins                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee........eeeeee.....eeeeeee.hhhh.eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeee...eeeeee.......eeeee..........eeeeeeeeeee.....eeee.hhh....eee..........eeeeeeeeee.hhhhhh.eeeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlw H    1 EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDYADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVTVSPASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK  228
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120       130|      142       152 ||||  167 ||    178 ||    189       199|||    212       222|   
                                                                              52A                            82A||               100A|||||                           130|                  154|||    169|      180|               200||              222|   
                                                                                                              82B|                100B||||                            133                   156||     171       182                203|               225   
                                                                                                               82C                 100C|||                                                   157|                                   205                     
                                                                                                                                    100D||                                                    162                                                           
                                                                                                                                     100E|                                                                                                                  
                                                                                                                                      100F                                                                                                                  


Chain K from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains d1zlwk1 K:2-107 automated matches                                                                         d1zlwk2 K:108-212 automated matches                                                                     SCOP domains
               CATH domains 1zlwK01 K:2-107 Immunoglobulins                                                                           1zlwK02 K:108-211 Immunoglobulins                                                                     - CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeeee.......eeeeee......eeeee...ee.......eeeee...eeeeeee..hhhhh.eeeeeeee..eeee...eeeee.......eeeee..hhhhhhhheeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeee.......eeeeee.......eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlw K    2 VVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPSRFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKYEKHKVYACEVTHQGLSSPVTKSFNRG  212
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181 ||    193       203         
                                                                                                                                                                                                               183|                          
                                                                                                                                                                                                                186                          


Chain L from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains d1zlwl1 L:2-107 automated matches                                                                         d1zlwl2 L:108-210 automated matches                                                                     SCOP domains
               CATH domains 1zlwL01 L:2-107 Immunoglobulins                                                                           1zlwL02 L:108-210 Immunoglobulins                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee..eeee....eeeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeeee..hhhhh.eeeeeeee..eeee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee....eeeeeee..ee....eeeee.........eeeeeeeeeehhhhhh...eeeeeee......eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlw L    2 VVMTQSPSTLSASVGDTITITCRASQSIETWLAWYQQKPGKAPKLLIYKASTLKTGVPSRFSGSGSGTEFTLTISGLQFDDFATYHCQHYAGYSATFGQGTRVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFN  210
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         


Chain M from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                  
               SCOP domains d1zlwm1 M:1-112 Immunoglobulin heavy chain variable domain, VH                                                            -d1zlwm2 M:114-227 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma        SCOP domains
               CATH domains 1zlwM01 M:1-113 Immunoglobulins                                                                                            1zlwM02 M:114-227 Immunoglobulins                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eeee....eeeeeeee..hhhhh.eeeeee.....eeeeeee.hhhh.eee.hhhh..eeeeee....eeeeee...hhhhheeeeeeee..........eeee...eeeeee...........eeeeeeeee................eee..........eeeeeeee...........eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1zlw M    1 EVQLVESGGGLVKAGGSLILSCGVSNFRISAHTMNWVRRVPGGGLEWVASISTSSTYRDYADAVKGRFTVSRDDLEDFVYLQMHKMRVEDTAIYYCARKGSDRLSDNDPFDAWGPGTVVTVSPASTKGPSVFAALGCLVKDYFPEPVTVSWNSALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP  227
                                    10        20        30        40        50  |     59        69        79   |||  86        96    ||100F       110       120 ||    145       156||||   172       183       193      |206       216     ||  
                                                                              52A                            82A||               100A|||||                   122|             154||||| 169|      180|               200||              222|  
                                                                                                              82B|                100B||||                    138              156||||  171       182                203|               225  
                                                                                                               82C                 100C|||                                      157|||                                205                    
                                                                                                                                    100D||                                       162||                                                       
                                                                                                                                     100E|                                        163|                                                       
                                                                                                                                      100F                                         165
   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  (4, 8)

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

(-) CATH Domains  (1, 8)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
Human (Homo sapiens) (912)
1a1zlwL02L:108-210
1b1zlwH02H:114-228
1c1zlwM02M:114-227
1d1zlwH01H:1-113
1e1zlwM01M:1-113
1f1zlwK02K:108-211
1g1zlwK01K:2-107
1h1zlwL01L:2-107

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1ZLW)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1ZLW)

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  1zlw
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 Related Entries

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(-) Related Entries Specified in the PDB File

1om3 1op3 1op5 1zls 1zlu 1zlv