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(-) Description

Title :  CRYSTAL STRUCTURE OF HCMV GB-NEUTRALIZING SM5-1 FAB FRAGMENT
 
Authors :  U. Diestel, Y. A. Muller
Date :  13 Feb 14  (Deposition) - 13 Aug 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.87
Chains :  Asym./Biol. Unit :  H,L
Keywords :  Immunoglobulin, Immune Response, Hcmv Neutralization, Hcmv Glycoprotein B, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Spindler, U. Diestel, J. D. Stump, A. K. Wiegers, T. H. Winkler, H. Sticht, M. Mach, Y. A. Muller
Structural Basis For The Recognition Of Human Cytomegalovirus Glycoprotein B By A Neutralizing Human Antibody.
Plos Pathog. V. 10 04377 2014
PubMed-ID: 25299639  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1004377

(-) Compounds

Molecule 1 - SM5-1 FAB HEAVY CHAIN
    Chains: H
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - SM5-1 FAB LIGHT CHAIN
    Chains: L
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : HL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric/Biological Unit (2, 9)
No.NameCountTypeFull Name
1FMT7Ligand/IonFORMIC ACID
2NA2Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN H:116 , ARG H:117 , TYR L:33 , SER L:35 , PHE L:50 , ASP L:51BINDING SITE FOR RESIDUE FMT H 301
2AC2SOFTWARETYR H:33 , TRP H:50 , ASN H:52 , LEU H:112 , HOH H:542BINDING SITE FOR RESIDUE FMT H 302
3AC3SOFTWARETYR H:60 , GLN H:65 , GLY H:66 , HOH H:458 , HOH H:459BINDING SITE FOR RESIDUE FMT H 303
4AC4SOFTWAREGLU H:10 , LYS H:19 , HOH H:444 , HOH H:534 , HOH H:535BINDING SITE FOR RESIDUE NA H 304
5AC5SOFTWARETHR H:103 , HOH H:496 , HOH H:524 , HOH H:525BINDING SITE FOR RESIDUE NA H 305
6AC6SOFTWARESER L:25 , SER L:26 , SER L:27 , LYS L:31 , ARG L:94BINDING SITE FOR RESIDUE FMT L 301
7AC7SOFTWAREALA H:186 , THR L:165 , THR L:166 , HOH L:532BINDING SITE FOR RESIDUE FMT L 302
8AC8SOFTWARELYS H:13 , SER H:133 , THR H:134 , PRO L:112 , LYS L:113BINDING SITE FOR RESIDUE FMT L 303
9AC9SOFTWARESER L:125 , GLU L:126BINDING SITE FOR RESIDUE FMT L 304

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:158 -H:214
3L:22 -L:89
4L:137 -L:196

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Phe H:164 -Pro H:165
2Glu H:166 -Pro H:167
3Tyr L:143 -Pro L:144

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OSU)

(-) 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:223
                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee...eee.....eeeeeeee..hhh.eeeeeeee.....eeeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeeeeeee............eeee...eeeee........eeeee....eeeeeeeeeee.....eeee.hhh....eee...ee.....eeeeeeeeee.hhh....eeeeeeehhhheeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4osu H   1 QVQLVQSGAEVRKPGASVKVSCKASGYSLKDHYMVWVRQAPGQGLEWMGWINPQSGGTGYGQKFQGRVTMTRDTSTNTAYMILSSLRSDDTAVYFCARDGAKTVSNSLLYYHNRLDAWGQGTMVTVSSASTKGPSVFPLAPSGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK 232
                                    10        20        30        40        50        60        70        80        90       100      |113       123       133       143 ||    159       169       179       189       199       209       219       229   
                                                                                                                                    107|                               145|                                                                                
                                                                                                                                     111                                152                                                                                


Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.....eeeeee...........eeeee.....eeeee.............eeeeee..eeeeee...hhhhheeeeeeeee...eeee...eeeee........eeeee..hhhhhhh..eeeeeeeeee.....eeeeee..eee...eee...ee.....eeeeeeeeehhhhhhhh..eeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4osu L   1 QSVLTQPPSVSAAPGQMVTISCSGSSSNIGKNYVSWYQQLPGAAPKLLIFDNNKRPSGTPDRFSGSKSGTSATLVITGLQTGDEADYYCGTPDRSLSVIFGGGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPT 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
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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 4OSU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  Cis Peptide Bonds
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 Related Entries

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(-) Related Entries Specified in the PDB File

4osn ANTIGEN IN UNBOUND FORM
4ot1