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(-) Description

Title :  CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR ME0386
 
Authors :  T. Stehle, J. Bauer
Date :  16 Apr 13  (Deposition) - 22 Oct 14  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
11P41Ligand/Ion3,3',3''-[NITRILOTRIS(METHANEDIYL-1H-1,2,3-TRIAZOLE-4,1-DIYL)]TRIPROPAN-1-OL
2ACT1Ligand/IonACETATE ION
3SIA3Ligand/IonO-SIALIC ACID
4ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:231 , GLU A:351 , HOH A:598 , HOH A:604 , HOH A:605BINDING SITE FOR RESIDUE ZN A 401
2AC2SOFTWARETYR A:312 , PRO A:317 , ASP A:318 , LYS A:345 , HOH A:519 , HOH A:590 , HOH A:621 , HOH A:622 , TYR B:308 , VAL B:322 , SER B:344 , 1P4 B:403 , HOH B:531 , HOH B:543BINDING SITE FOR RESIDUE SIA A 402
3AC3SOFTWAREHIS B:231 , GLU B:351 , HOH B:622BINDING SITE FOR RESIDUE ZN B 401
4AC4SOFTWARETYR B:312 , PRO B:317 , ASP B:318 , LYS B:345 , 1P4 B:403 , HOH B:506 , HOH B:595 , HOH B:627 , HOH B:629 , HOH B:630 , TYR C:308 , VAL C:322 , HOH C:648 , HOH C:655BINDING SITE FOR RESIDUE SIA B 402
5AC5SOFTWARESIA A:402 , SIA B:402 , SIA C:402BINDING SITE FOR RESIDUE 1P4 B 403
6AC6SOFTWAREHIS C:231 , ACT C:403BINDING SITE FOR RESIDUE ZN C 401
7AC7SOFTWARETYR A:308 , VAL A:322 , HOH A:614 , HOH A:623 , 1P4 B:403 , TYR C:312 , PRO C:317 , ASP C:318 , PRO C:320 , LYS C:345 , HOH C:649 , HOH C:660 , HOH C:662BINDING SITE FOR RESIDUE SIA C 402
8AC8SOFTWAREHIS C:231 , ILE C:232 , ZN C:401BINDING SITE FOR RESIDUE ACT C 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K6U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4K6U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K6U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K6U)

(-) Exons   (0, 0)

(no "Exon" information available for 4K6U)

(-) 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......ee.........eeeeeeee.................eeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.......ee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k6u 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:187
                                                                                                                                                                                                                           
               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
                 4k6u B 179 PKYDTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       


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
                 4k6u 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 4K6U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K6U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K6U)

(-) 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 4k6v 4k6w 4xqa 4xqb

(-) Related Entries Specified in the PDB File

1uxe CRYSTAL STRUCTURE OF UNLIGANDED AD37 FIBER KNOB
3n0i CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH BIVALENT GLYCAN RECEPTOR
3qnd CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT INHIBITOR
4k6t
4k6v
4k6w