3QND - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF AD37 FIBER KNOB IN COMPLEX WITH TRIVALENT SIALIC ACID INHIBITOR

Authors :   T. Stehle, J. Bauer, M. Elofsson

Date :   08 Feb 11 (Deposition) - 15 Jun 11 (Release) - 10 Aug 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A,B,C,E,F,G
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: E,F,G  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),E (1x),F (1x),G (1x)

Keywords :   Fiber Knob, Protein Carbohydrate Interaction, Carbohydrate Mimetic, Multivalent Ligand, Viral Protein-Inhibitor Complex, Cell Adhesion- Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Spjut, W. Qian, J. Bauer, R. Storm, L. Frangsmyr, T. Stehle, N. Arnberg, M. Elofsson
A Potent Trivalent Sialic Acid Inhibitor Of Adenovirus Type 37 Infection Of Human Corneal Cells.
Angew. Chem. Int. Ed. Engl. V. 50 6519 2011
PubMed-ID: 21648036 | Reference-DOI: 10.1002/ANIE.201101559

Molecule 1 - FIBER PROTEIN
	Chains	:	A, B, C, E, F, G
	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	:	UNP RESIDUES 177-365
	Gene	:	L5
	Organism Scientific	:	HUMAN ADENOVIRUS 37
	Organism Taxid	:	52275
	Synonym	:	FIBER PROTEIN

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	E	F	G
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				E	F	G
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	E (1x)	F (1x)	G (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	SIA	6	Ligand/Ion	O-SIALIC ACID
2	ZN	7	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	SIA	3	Ligand/Ion	O-SIALIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	SIA	3	Ligand/Ion	O-SIALIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 3)

No.	Name	Count	Type	Full Name
1	SIA	3	Ligand/Ion	O-SIALIC ACID
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HOH A:13 , HIS A:231 , GLU A:351	BINDING SITE FOR RESIDUE ZN A 7
02	AC2	SOFTWARE	HOH A:126 , TYR A:312 , PRO A:317 , ASP A:318 , PRO A:320 , LYS A:345 , HOH B:71 , TYR B:308 , SER B:344	BINDING SITE FOR RESIDUE SIA A 1
03	AC3	SOFTWARE	HOH B:78 , HIS B:231 , GLU B:351 , HOH C:452	BINDING SITE FOR RESIDUE ZN B 8
04	AC4	SOFTWARE	TYR B:312 , PRO B:317 , ASP B:318 , PRO B:320 , LYS B:345 , HOH B:433 , TYR C:308	BINDING SITE FOR RESIDUE SIA B 1
05	AC5	SOFTWARE	HIS C:231 , GLU C:351	BINDING SITE FOR RESIDUE ZN C 9
06	AC6	SOFTWARE	HOH A:48 , TYR A:308 , HOH C:167 , TYR C:312 , PRO C:317 , ASP C:318 , PRO C:320 , LYS C:345	BINDING SITE FOR RESIDUE SIA C 1
07	AC7	SOFTWARE	ASP A:258 , GLU E:281	BINDING SITE FOR RESIDUE ZN E 10
08	AC8	SOFTWARE	HOH E:6 , HOH E:89 , HIS E:231 , GLU E:351	BINDING SITE FOR RESIDUE ZN E 7
09	AC9	SOFTWARE	HOH E:101 , HOH E:165 , TYR E:312 , PRO E:317 , ASP E:318 , PRO E:320 , LYS E:345 , HOH E:469 , TYR F:308	BINDING SITE FOR RESIDUE SIA E 1
10	BC1	SOFTWARE	HIS F:231 , GLU F:351 , HOH F:390 , HOH G:12	BINDING SITE FOR RESIDUE ZN F 8
11	BC2	SOFTWARE	HOH F:103 , TYR F:312 , PRO F:317 , ASP F:318 , LYS F:345 , HOH F:384 , TYR G:308 , VAL G:322 , SER G:344	BINDING SITE FOR RESIDUE SIA F 1
12	BC3	SOFTWARE	HOH E:166 , HOH G:82 , HIS G:231 , GLU G:351	BINDING SITE FOR RESIDUE ZN G 9
13	BC4	SOFTWARE	HOH E:8 , TYR E:308 , VAL E:322 , TYR G:312 , PRO G:317 , ASP G:318 , PRO G:320 , LYS G:345 , HOH G:391	BINDING SITE FOR RESIDUE SIA G 1

(no "SS Bond" information available for 3QND)

(no "Cis Peptide Bond" information available for 3QND)

(no "SAP(SNP)/Variant" information available for 3QND)

(no "PROSITE Motif" information available for 3QND)

(no "Exon" information available for 3QND)

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 A from PDB  Type:PROTEIN  Length:184
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:184
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q64823_9ADEN   182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d3qnda_ A: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee................eeeeeeeeee..eeeeeeeeee......eee........eeeeeeee.................ee.............hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.....eeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnd 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
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:185
                                   190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360     
         Q64823_9ADEN   181 YDTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d3qndb_ B: automated matches                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee................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
                 3qnd 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
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:183
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362   
         Q64823_9ADEN   183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d3qndc_ C: automated matches                                                                                                                                                            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
                 3qnd C 183 TRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362

Chain E from PDB  Type:PROTEIN  Length:184
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:184
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q64823_9ADEN   182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d3qnde_ E: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee................eeeeeeeeee..eeeeeeeeee......ee.........eeeeeeee............hhhhheeee..ee.......hhhhh..............hhh.eeeeeee.hhh...eeeeeeee.......eeeeeeee.......ee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnd E 182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361

Chain F from PDB  Type:PROTEIN  Length:184
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:184
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q64823_9ADEN   182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d3qndf_ F: automated matches                                                                                                                                                             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
                 3qnd F 182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361

Chain G from PDB  Type:PROTEIN  Length:184
 aligned with Q64823_9ADEN | Q64823 from UniProtKB/TrEMBL  Length:365

    Alignment length:184
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
         Q64823_9ADEN   182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
               SCOP domains d3qndg_ G: automated matches                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----Adeno_knob-3qndG01 G:186-361                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) ----Adeno_knob-3qndG02 G:186-361                                                                                                                                                    ---- Pfam domains (2)
           Pfam domains (3) ----Adeno_knob-3qndG03 G:186-361                                                                                                                                                    ---- Pfam domains (3)
           Pfam domains (4) ----Adeno_knob-3qndG04 G:186-361                                                                                                                                                    ---- Pfam domains (4)
           Pfam domains (5) ----Adeno_knob-3qndG05 G:186-361                                                                                                                                                    ---- Pfam domains (5)
           Pfam domains (6) ----Adeno_knob-3qndG06 G:186-361                                                                                                                                                    ---- Pfam domains (6)
         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
                 3qnd G 182 DTRTLWTTPDTSPNCTIAQDKDSKLTLVLTKCGSQILANVSLIVVAGKYHIINNKTNPKIKSFTIKLLFNKNGVLLDNSNLGKAYWNFRSGNSNVSTAYEKAIGFMPNLVAYPKPSNSKKYARDIVYGTIYLGGKPDQPAVIKTTFNQETGCEYSITFNFSWSKTYENVEFETTSFTFSYIAQE 365
                                   191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Virus attachment protein globular domain (47)

Superfamily: Virus attachment protein globular domain (47)

Family: Adenovirus fiber protein knob domain (27)

Protein domain: automated matches (13)

Human adenovirus 37 [TaxId: 52275] (6)

1a	d3qnda_	A:
1b	d3qndb_	B:
1c	d3qndc_	C:
1d	d3qnde_	E:
1e	d3qndf_	F:
1f	d3qndg_	G:

(no "CATH Domain" information available for 3QND)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Reo_sigma (16)

Family: Adeno_knob (11)

Human adenovirus 37 (5)

1a	Adeno_knob-3qndG01	G:186-361
1b	Adeno_knob-3qndG02	G:186-361
1c	Adeno_knob-3qndG03	G:186-361
1d	Adeno_knob-3qndG04	G:186-361
1e	Adeno_knob-3qndG05	G:186-361
1f	Adeno_knob-3qndG06	G:186-361

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,E,F,G (Q64823_9ADEN | Q64823)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0019058	viral life cycle	A set of processes which all viruses follow to ensure survival; includes attachment and entry of the virus particle, decoding of genome information, translation of viral mRNA by host ribosomes, genome replication, and assembly and release of viral particles containing the genome.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.

Asymmetric Unit
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	Cis Peptide Bonds
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	3qnd
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	Q64823_9ADEN \| Q64823
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	Q64823_9ADEN \| Q64823	:	2j12
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	Q64823_9ADEN \| Q64823	:	1uxa 1uxe 2wbw 2wgt 2wgu 3n0i 4k6t 4k6u 4k6v 4k6w 4xqa 4xqb

(no "Related Entries Specified in the PDB File" available for 3QND)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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