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(-) Description

Title :  CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0407
 
Authors :  T. Stehle, J. Bauer
Date :  16 Apr 13  (Deposition) - 22 Oct 14  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Adenovirus, Fiber Knob, Protein Carbohydrate Interaction, Carbohydrate Mimic, Multivalent Ligand, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Caraballo, M. Saleeb, J. Bauer, A. M. Liaci, N. Chandra, R. J. Storm, L. Frangsmyr, W. Qian, T. Stehle, N. Arnberg, M. Elofsson
Triazole Linker-Based Trivalent Sialic Acid Inhibitors Of Adenovirus Type 37 Infection Of Human Corneal Epithelial Cells.
Org. Biomol. Chem. V. 13 9194 2015
PubMed-ID: 26177934  |  Reference-DOI: 10.1039/C5OB01025J

(-) Compounds

Molecule 1 - FIBER PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPROEX HTB
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: FIBER KNOB
    Gene: L5
    Organism Scientific: HUMAN ADENOVIRUS 37
    Organism Taxid: 52275

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 15)

Asymmetric/Biological Unit (6, 15)
No.NameCountTypeFull Name
118D3Ligand/Ion3,5-DIDEOXY-5-(PROPANOYLAMINO)-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC ACID
21P41Ligand/Ion3,3',3''-[NITRILOTRIS(METHANEDIYL-1H-1,2,3-TRIAZOLE-4,1-DIYL)]TRIPROPAN-1-OL
3ACT4Ligand/IonACETATE ION
4CL3Ligand/IonCHLORIDE ION
5NA1Ligand/IonSODIUM ION
6ZN3Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:231 , GLU A:351 , HOH A:690 , HOH A:691 , ACT B:403BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWARETYR A:312 , PRO A:317 , ASP A:318 , PRO A:320 , LYS A:345 , 1P4 A:403 , HOH A:609 , HOH A:611 , HOH A:612 , HOH A:615 , HOH A:618 , HOH A:622 , HOH A:663 , SER B:344 , HOH B:596BINDING SITE FOR RESIDUE 18D A 402
03AC3SOFTWARE18D A:402 , HOH A:661 , 18D B:402 , 18D C:402BINDING SITE FOR RESIDUE 1P4 A 403
04AC4SOFTWAREILE A:198 , LYS A:229 , TYR A:230 , HOH A:524 , HOH A:674BINDING SITE FOR RESIDUE ACT A 404
05AC5SOFTWAREGLY A:263 , LYS A:264BINDING SITE FOR RESIDUE CL A 405
06AC6SOFTWAREHIS B:231 , GLU B:351 , HOH B:574 , HOH B:680BINDING SITE FOR RESIDUE ZN B 401
07AC7SOFTWARE1P4 A:403 , TYR B:312 , PRO B:317 , ASP B:318 , PRO B:320 , LYS B:345 , HOH B:590 , HOH B:599 , HOH B:600 , HOH B:601 , HOH B:655 , HOH B:656 , HOH B:657 , HOH C:636BINDING SITE FOR RESIDUE 18D B 402
08AC8SOFTWAREHIS A:231 , GLU A:351 , ZN A:401 , HOH A:623 , HOH A:690 , HOH A:691 , LYS B:300 , TYR B:302BINDING SITE FOR RESIDUE ACT B 403
09AC9SOFTWAREASN B:238 , LYS B:240BINDING SITE FOR RESIDUE CL B 404
10BC1SOFTWAREHIS C:231 , ACT C:404BINDING SITE FOR RESIDUE ZN C 401
11BC2SOFTWARE1P4 A:403 , HOH A:606 , TYR C:312 , PRO C:317 , ASP C:318 , PRO C:320 , LYS C:345 , HOH C:638 , HOH C:639 , HOH C:643 , HOH C:644 , HOH C:694BINDING SITE FOR RESIDUE 18D C 402
12BC3SOFTWAREILE C:198 , LYS C:229 , TYR C:230 , HOH C:516 , HOH C:654BINDING SITE FOR RESIDUE ACT C 403
13BC4SOFTWAREHIS C:231 , ILE C:232 , ZN C:401 , HOH C:608BINDING SITE FOR RESIDUE ACT C 404
14BC5SOFTWAREARG C:184BINDING SITE FOR RESIDUE CL C 405
15BC6SOFTWAREASP C:318BINDING SITE FOR RESIDUE NA C 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K6V)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K6V)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K6V)

(-) Exons   (0, 0)

(no "Exon" information available for 4K6V)

(-) 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 A from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee.................eeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k6v A 182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    


Chain B from PDB  Type:PROTEIN  Length:185
                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee.................eeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k6v B 181 YDTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     


Chain C from PDB  Type:PROTEIN  Length:183
                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee............hhhhheeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k6v C 183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362
   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  (0, 0)

(no "SCOP Domain" information available for 4K6V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K6V)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q64823_9ADEN | Q64823: 2j12
UniProtKB/TrEMBL
        Q64823_9ADEN | Q64823: 1uxa 1uxe 2wbw 2wgt 2wgu 3n0i 3qnd 4k6t 4k6u 4k6w 4xqa 4xqb

(-) Related Entries Specified in the PDB File

3qnd CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT INHIBITOR
1uxe CRYSTAL STRUCTURE OF UNLIGANDED AD37 FIBER KNOB
3n0i CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH BIVALENT GLYCAN RECEPTOR
4k6t
4k6u
4k6w