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(-) Description

Title :  BACTERICIDAL ANTIBODY AGAINST NEISSERIA MENINGITIDIS
 
Authors :  J. M. H. Van Den Elsen, J. N. Herron, J. Kroon, P. Gros
Date :  26 Feb 97  (Deposition) - 04 Sep 97  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  H,L,P
Biol. Unit 1:  H,L,P  (1x)
Biol. Unit 2:  H (1x),L (1x),P (1x)
Keywords :  Murine Immunoglobulin Igg2A Kappa, Bactericidal Antibody, Epitope P1. 16 Of Pora From Neisseria Meningitidis, Complex (Immunoglobulin/Peptide) (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Van Den Elsen, J. N. Herron, P. Hoogerhout, J. T. Poolman, E. Boel, T. Logtenberg, J. Wilting, D. J. Crommelin, J. Kroon, P. Gros
Bactericidal Antibody Recognition Of A Pora Epitope Of Neisseria Meningitidis: Crystal Structure Of A Fab Fragment In Complex With A Fluorescein-Conjugated Peptide.
Proteins V. 29 113 1997 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - MN12H2 IGG2A-KAPPA
    Cell: B-LYMPHOCYTE HYBRIDOMA
    Chains: L
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: MN12H2 MURINE-MURINE HYBRIDOMA CELL LINE
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 2 - MN12H2 IGG2A-KAPPA
    Cell: B-LYMPHOCYTE HYBRIDOMA
    Chains: H
    Engineered: YES
    Expression System: MUS MUSCULUS
    Expression System Cell Line: MN12H2 MURINE-MURINE HYBRIDOMA CELL LINE
    Expression System Common: HOUSE MOUSE
    Expression System Taxid: 10090
    Fragment: FAB FRAGMENT
    Organism Common: HOUSE MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Strain: BALB/C
 
Molecule 3 - PORA P1.16 PEPTIDE FLUORESCEIN CONJUGATE
    Chains: P
    Engineered: YES
    Fragment: APEX OF EXTRACELLULAR LOOP 4 (VR2) OF PORA, RESIDUES 180 - 187
    Synonym: P1.16, AC-TKDTNNNLC(FLUORESCEIN)-NH2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : HLP
Biological Unit 1 (1x): HLP
Biological Unit 2 (1x): H (1x)L (1x)P (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric Unit (3, 3)
No.NameCountTypeFull Name
1CD1Ligand/IonCADMIUM ION
2CYF1Mod. Amino Acid5-[2-(2-AMINO-2-CARBAMOYL-ETHYLSULFANYL)-ACETYLAMINO]-2-(3,6-DIHYDROXY-9,9A-DIHYDRO-3H-XANTHEN-9-YL)-BENZOIC ACID
3THC1Mod. Amino AcidN-METHYLCARBONYLTHREONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CYF1Mod. Amino Acid5-[2-(2-AMINO-2-CARBAMOYL-ETHYLSULFANYL)-ACETYLAMINO]-2-(3,6-DIHYDROXY-9,9A-DIHYDRO-3H-XANTHEN-9-YL)-BENZOIC ACID
3THC1Mod. Amino AcidN-METHYLCARBONYLTHREONINE
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2CYF-1Mod. Amino Acid5-[2-(2-AMINO-2-CARBAMOYL-ETHYLSULFANYL)-ACETYLAMINO]-2-(3,6-DIHYDROXY-9,9A-DIHYDRO-3H-XANTHEN-9-YL)-BENZOIC ACID
3THC-1Mod. Amino AcidN-METHYLCARBONYLTHREONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS L:98 , HOH L:222 , HOH L:224BINDING SITE FOR RESIDUE CD L 220
2CDBUNKNOWNHIS L:98CD BINDING SITE.

(-) SS Bonds  (5, 5)

Asymmetric Unit
No.Residues
1H:22 -H:96
2H:148 -H:203
3L:23 -L:93
4L:139 -L:199
5L:219 -H:136

(-) Cis Peptide Bonds  (5, 5)

Asymmetric Unit
No.Residues
1Thr L:7 -Pro L:8
2Val L:99 -Pro L:100
3Tyr L:145 -Pro L:146
4Phe H:154 -Pro H:155
5Trp H:196 -Pro H:197

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MPA)

(-) 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 Q569X1_MOUSE | Q569X1 from UniProtKB/TrEMBL  Length:476

    Alignment length:227
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       
         Q569X1_MOUSE    20 EVQLLQSGTELVRPGASVKLSCTASGFSIKDSLLHWVMQRPEQGLEWIGWIDPEDGETKYVPKFQDKATLTAATSSNTAYLQLSSLTSGDTATYYCLFYGYDDGRDYFDYWGQGTTITVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTI 246
               SCOP domains d1mpah1 H:1-121 Immunoglobulin heavy chain variable domain, VH                                                           d1mpah2 H:122-225 Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma                            SCOP domains
               CATH domains 1mpaH01 H:1-121 Immunoglobulins                                                                                          1mpaH02 H:122-220 Immunoglobulins                                                                  ------- CATH domains
               Pfam domains V-set-1mpaH02 H:1-119                                                                                                  --------------C1-set-1mpaH01 H:134-215                                                          ------------ Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee.......eeeeeee.....eeeeeeee....eeee.......eeeeee....eeeeee.........eeeeeeee.......eeee.....eee........eeeee..........eeeeeeeeeee.....eeee........eeee........eeeeeeeeee..hhhhh..eeeeee....eeeeee......--.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mpa H   1 EVNLQQSGTVLARPGASVRMSCKASGYSFTSYWLHWIKQRPGQGLEWIGGIYPGNRDTRYTQRFKDKAKLTAVTSANTAYMELSSLTNEDSAVYYCSIIYFDYADFIMDYWGQGTTVTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGP--TI 225
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |  | 
                                                                                                                                                                                                                                                        223  | 
                                                                                                                                                                                                                                                           224 


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

    Alignment length:219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         
         A2NHM3_MOUSE     1 DVLMTQTPLSLPVSLGDQASISCRSSQSIVHTNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
               SCOP domains d1mpal1 L:1-112 Immunoglobulin light chain kappa variable domain, VL-kappa                                      d1mpal2 L:113-219 Immunoglobulin light chain kappa constant domain, CL-kappa                                SCOP domains
               CATH domains 1mpaL01 L:1-113 Immunoglobulins                                                                                  1mpaL02 L:114-216 Immunoglobulins                                                                      --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeeee....eeeeeee............eeeeee......eeee.............eeeeee..eeeeee.........eeeeee............eeeee......eeeee...hhhhhh.eeeeeeeee......eeeeee.........eeeeee.........eeeeeeeeehhhhh...eeeeeeee......eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mpa L   1 DIVMTQTPLSLPVSLGDKASISCRSSQALVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVFFCSQSTHVPRTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC 219
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210         


Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 1mpa P   1 tKDTNNNLc   9
                            |       |
                            |       9-CYF
                            1-THC
   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, 4)

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

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: Ig (577)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain H   (Q569X1_MOUSE | Q569X1)

Chain L   (A2NHM3_MOUSE | A2NHM3)

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  1mpa
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
        GCAA_MOUSE | P01863: 1dqm 1dqq 1ehl 1fe8 1ggi 1igt 1keg 1kn2 1kn4 1kno 1mh5 1mnu 1ob1 1pg7 1uyw 1yec 1yef 1yeg 1yeh 1yei 1yej 1yek 2ipu 2mpa 2r0w 2r0z 2r29 2r69 2r6p 2vl5 2zch 2zck 2zcl 3bgf 3oz9 3zo0 4f37 5vaa
        Q569X1_MOUSE | Q569X1: 5ikc
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1nbv 1plg 1pz5 1qfu 1t2q 1zea 2a1w 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
        Q569X1_MOUSE | Q569X1: 2mpa

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1MPA)