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(-) Description

Title :  FAB COMPLEX WITH METHOTREXATE
 
Authors :  K. L. Longenecker, R. A. Judge, S. Gayda, S. Manoj, S. Saldana, Q. Ruan, K S. Tetin
Date :  09 Jan 14  (Deposition) - 02 Jul 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Igg1/K Family, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gayda, K. L. Longenecker, S. Manoj, R. A. Judge, S. C. Saldana, Q. Ruan, K. M. Swift, S. Y. Tetin
Water Channel In The Binding Site Of A High Affinity Anti-Methotrexate Antibody.
Biochemistry V. 53 3719 2014
PubMed-ID: 24832237  |  Reference-DOI: 10.1021/BI5001382

(-) Compounds

Molecule 1 - FAB ADD056 HEAVY CHAIN
    Chains: H
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HUMAN EMBRYONIC KIDNEY CELLS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
 
Molecule 2 - FAB ADD056 LIGHT CHAIN
    Chains: L
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HUMAN EMBRYONIC KIDNEY CELLS
    Expression System Common: HUMAN
    Expression System Taxid: 9606
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MT11Ligand/IonN-(4-{[(2,4-DIAMINOPTERIDIN-1-IUM-6-YL)METHYL](METHYL)AMINO}BENZOYL)-L-GLUTAMIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO H:32 , TYR H:33 , ALA H:34 , ASN H:36 , TYR H:51 , TYR H:99 , HIS L:31 , TYR L:37 , GLU L:39 , TYR L:41 , PHE L:94 , GLY L:96 , LEU L:101 , HOH L:465 , HOH L:482 , HOH L:496 , HOH L:563BINDING SITE FOR RESIDUE MT1 L 301

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:143 -H:198
3L:23 -L:93
4L:139 -L:199

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Pro H:32 -Tyr H:33
2Phe H:149 -Pro H:150
3Glu H:151 -Pro H:152
4Gln H:174 -Ser H:175
5Trp H:191 -Pro H:192
6Ile L:7 -Pro L:8
7Val L:99 -Pro L:100
8Tyr L:145 -Pro L:146
9Thr L:207 -Ser L:208

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OCX)

(-) 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:210
                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee........eeeeeee.....eeeeeeee....eee.......eeeeee....eeeeee...hhhhheeeeeeeee..eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhhhhh.eee...ee....eeeeeeeeee.........eeeeeehhhheeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ocx H   1 DVQLQESGPGLVKPSQSLSLTCTVTGFSITSPYAWNWIRQFPGNTLEWMGYISYRGSTTYHPSLKSRISITRDTSKNQFFLQLNSVTTEDTATYFCSSYGNYGAYSGQGTLVTVSAAKTTPPSVYPLAPGSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130|      146       156       166       176       186       196       206       216
                                                                                                                                                           130|                                                                               
                                                                                                                                                            137                                                                               


Chain L from PDB  Type:PROTEIN  Length:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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.........eeeeeeeeeehhhhh...eeeeeee.....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ocx L   1 DVLLTQIPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSTRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPLTFGAGTQLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSPIVKSFNR 216
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200   ||  212    
                                                                                                                                                                                                                                     204|         
                                                                                                                                                                                                                                      207
   Legend:   → Mismatch (orange background)
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  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  (0, 0)

(no "SCOP Domain" information available for 4OCX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4OCX)

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  Cis Peptide Bonds
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    Trp H:191 - Pro H:192   [ RasMol ]  
    Tyr L:145 - Pro L:146   [ RasMol ]  
    Val L:99 - Pro L:100   [ RasMol ]  
 

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  4ocx
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 Related Entries

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

UniProtKB/Swiss-Prot
        A2NHM3_MOUSE | A2NHM3: 4p3d
UniProtKB/TrEMBL
        A2NHM3_MOUSE | A2NHM3: 1cbv 1f3d 1lo0 1m71 1m7d 1m7i 1mnu 1mpa 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 4ocy 4q0x 4tpr 4tqe

(-) Related Entries Specified in the PDB File

4ocy