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(-) Description

Title :  ANTI-COCAINE ANTIBODY 7.5.21, CRYSTAL FORM I
 
Authors :  E. Pozharski, A. Hewagama, A. Shanafelt, D. Ringe, G. A. Petsko
Date :  21 Jun 05  (Deposition) - 28 Jun 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  H,I,L,M
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  I,M  (1x)
Biol. Unit 3:  H,I,L,M  (2x)
Biol. Unit 4:  H (2x),I (2x),L (2x),M (2x)
Biol. Unit 5:  H,I,L,M  (1x)
Biol. Unit 6:  H (1x),I (1x),L (1x),M (1x)
Keywords :  Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Pozharski, A. Hewagama, A. Shanafelt, D. Ringe, G. A. Petsko
Flexibility Of Packing: Four Crystal Forms Of An Anti-Cocaine Antibody 7. 5. 21
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - IMMUNOGLOBULIN LIGHT CHAIN KAPPA
    Cell Line: HYBRIDOMA
    Chains: L, M
    Fragment: FAB FRAGMENT, LIGHT CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - IMMUNOGLOBULIN HEAVY CHAIN
    Cell Line: HYBRIDOMA
    Chains: H, I
    Fragment: FAB FRAGMENT, HEAVY CHAIN
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : HILM
Biological Unit 1 (1x): H L 
Biological Unit 2 (1x):  I M
Biological Unit 3 (2x): HILM
Biological Unit 4 (2x): H (2x)I (2x)L (2x)M (2x)
Biological Unit 5 (1x): HILM
Biological Unit 6 (1x): H (1x)I (1x)L (1x)M (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric Unit (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 3 (1, 14)
No.NameCountTypeFull Name
1SO414Ligand/IonSULFATE ION
Biological Unit 4 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
Biological Unit 5 (1, 7)
No.NameCountTypeFull Name
1SO47Ligand/IonSULFATE ION
Biological Unit 6 (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE I:27 , THR I:28 , TYR I:32 , HOH I:275 , PRO L:64 , ASP L:65 , ARG L:66 , ARG L:82BINDING SITE FOR RESIDUE SO4 I 226
2AC2SOFTWARETYR I:108 , LYS L:31 , SER L:32 , SER L:97 , HIS L:98BINDING SITE FOR RESIDUE SO4 L 217
3AC3SOFTWARELYS M:31 , SER M:32 , SER M:97 , HIS M:98BINDING SITE FOR RESIDUE SO4 M 217
4AC4SOFTWAREARG I:87 , SER I:88 , GLU I:89BINDING SITE FOR RESIDUE SO4 I 227
5AC5SOFTWAREPRO I:14 , ARG I:87 , SER I:88 , GLU I:89 , SER I:122 , SER I:123 , HOH I:262 , HOH I:267 , HOH I:276BINDING SITE FOR RESIDUE SO4 I 228
6AC6SOFTWARETHR L:187 , ASP L:189 , GLU L:190 , ARG L:193BINDING SITE FOR RESIDUE SO4 L 218
7AC7SOFTWAREASN M:150 , HIS M:203 , LYS M:204BINDING SITE FOR RESIDUE SO4 M 218

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:150 -H:205
3I:22 -I:96
4I:150 -I:205
5L:23 -L:93
6L:139 -L:199
7M:23 -M:93
8M:139 -M:199

(-) Cis Peptide Bonds  (14, 14)

Asymmetric Unit
No.Residues
1Ser L:7 -Pro L:8
2Ile L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Lys L:204 -Thr L:205
5Gly H:104 -Lys H:105
6Phe H:156 -Pro H:157
7Glu H:158 -Pro H:159
8Trp H:198 -Pro H:199
9Ser M:7 -Pro M:8
10Ile M:99 -Pro M:100
11Tyr M:145 -Pro M:146
12Phe I:156 -Pro I:157
13Glu I:158 -Pro I:159
14Trp I:198 -Pro I:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A1W)

(-) Exons   (0, 0)

(no "Exon" information available for 2A1W)

(-) 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:225
 aligned with Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:225
                                                                                                                                   122                                                                                                                       
                                                                                                                                121  |                                                                                                                       
                                                                                                                             118  |  |                                                                                                                       
                                                                                                                           117 |  |  |                                                                                                                       
                                    29        39        49        59        69        79        89        99       109       118  |  | 126       136       146       156       166       176       186       196       206       216       226       236     
         Q99LC4_MOUSE    20 QVQLQQSGAELARPGASVRLSCKASGYTFTGYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCAR-SSYY--SYDLFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 241
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------d2a1wh1 H:124-225 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 2a1wH01 H:1-123 Immunoglobulins                                                                                            2a1wH02 H:124-224 Immunoglobulins                                                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......ee........eeeeee....eeeeee...hhhhheeeeeeeeee..........ee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a1w H   1 DVKLVESGGGLVKPGGSLRLSCAASGFTFRNYGMSWVRQTPEKRLEWVAAISGNSLYTSYPDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYFCARHDDYYGKSPYFFDVWGAGTTVTASSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     


Chain I from PDB  Type:PROTEIN  Length:225
 aligned with Q99LC4_MOUSE | Q99LC4 from UniProtKB/TrEMBL  Length:463

    Alignment length:225
                                                                                                                                   122                                                                                                                       
                                                                                                                                121  |                                                                                                                       
                                                                                                                             118  |  |                                                                                                                       
                                                                                                                           117 |  |  |                                                                                                                       
                                    29        39        49        59        69        79        89        99       109       118  |  | 126       136       146       156       166       176       186       196       206       216       226       236     
         Q99LC4_MOUSE    20 QVQLQQSGAELARPGASVRLSCKASGYTFTGYGVSWVKQRTGQGLEWVGEIYPGSGNTYYSEKFKGKATLTTDKSSSTAYMHLSSLTSEDSAVYFCAR-SSYY--SYDLFAYWGQGTLVTVSAAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 241
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------d2a1wi1 I:124-225 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                        SCOP domains
               CATH domains 2a1wI01 I:1-123 Immunoglobulins                                                                                            2a1wI02 I:124-224 Immunoglobulins                                                                    - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee..hhhhh.eeeeee.....eeeeeee......ee........eeeeeehhh.eeeeee...hhhhheeeeeeee..........eeee...eeeee........eeeee..........eeeeeeeeeee.....eeee.hhh....eee...eee..eeeeeeeeeee.hhhhhh..eeeeeehhhheeeeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a1w I   1 DVKLVESGGGLVKPGGSLRLSCAASGFTFRNYGMSWVRQTPEKRLEWVAAISGNSLYTSYPDSVKGRFTISRDNAKNNLYLQMSSLRSEDTALYFCARHDDYYGKSPYFFDVWGAGTTVTASSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRDC 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220     


Chain L from PDB  Type:PROTEIN  Length:216
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
               SCOP domains d2a1wl1 L:1-113 automated matches                                                                                d2a1wl2 L:114-216 automated matches                                                                     SCOP domains
               CATH domains 2a1wL01 L:1-113 Immunoglobulins                                                                                  -2a1wL02 L:115-214 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeee...eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhh..eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a1w L   1 DVLMTQSPLSLPVSLGDQASISCRCSQSIVKSNGHTYLEWYLQKPGRSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLRISRVEAEDLGVYYCFQGSHIPWTFGGGTKLESKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      


Chain M from PDB  Type:PROTEIN  Length:216
 aligned with A2NHM3_MOUSE | A2NHM3 from UniProtKB/TrEMBL  Length:219

    Alignment length:216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210      
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
               SCOP domains d2a1wm1 M:1-113 automated matches                                                                                d2a1wm2 M:114-216 automated matches                                                                     SCOP domains
               CATH domains 2a1wM01 M:1-113 Immunoglobulins                                                                                  -2a1wM02 M:115-214 Immunoglobulins                                                                   -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee............eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..eee...eeeee.........eeeeeeeeeehhhhhh...eeeeee.......eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2a1w M   1 DVLMTQSPLSLPVSLGDQASISCRCSQSIVKSNGHTYLEWYLQKPGRSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLRISRVEAEDLGVYYCFQGSHIPWTFGGGTKLESKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 6)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)
(-)
Architecture: Sandwich (5577)
(-)
Topology: Immunoglobulin-like (3897)
(-)
Homologous Superfamily: Immunoglobulins (2282)
(-)
House mouse (Mus musculus) (616)
1a2a1wL02L:115-214
1b2a1wH02H:124-224
1c2a1wI02I:124-224
1d2a1wL01L:1-113
1e2a1wM01M:1-113
1f2a1wH01H:1-123
1g2a1wI01I:1-123
1h2a1wM02M:115-214

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A1W)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2A1W)

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  2a1w
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  Q99LC4_MOUSE | Q99LC4
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
        Q99LC4_MOUSE | Q99LC4: 1afv 3hkf
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2dqt 2dqu 2dtm 2ipt 2ipu 2iq9 2iqa 2mpa 2ojz 2ok0 2r0w 2r0z 3bae 3bkc 3bkj 3bkm 3bqu 3eys 3eyu 3uo1 3uyr 3v4u 3v52 3we6 4f37 4hdi 4ocx 4ocy 4q0x 4tpr 4tqe
        Q99LC4_MOUSE | Q99LC4: 1ae6 1e6j 1f58 1gig 1jhk 1jnl 1jnn 2ntf 2vir 2vis 2vit 4q0x

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2A1W)