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Title :   CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH GLUCOSE

Authors :   N. E. Ziolkowska, A. Wlodawer

Date :   09 Nov 06 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A,B

Keywords :   Griffithsin, Lectins, Domain Swapping, Mannose Binding, Hiv, Sars, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. E. Ziolkowska, S. R. Shenoy, B. R. O'Keefe, A. Wlodawer
Crystallographic Studies Of The Complexes Of Antiviral Protein Griffithsin With Glucose And N-Acetylglucosamine.
Protein Sci. V. 16 1485 2007
PubMed-ID: 17567736 | Reference-DOI: 10.1110/PS.072889407

Molecule 1 - GRIFFITHSIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	NICOTIANA BENTHAMIANA
	Expression System Taxid	:	4100
	Organism Scientific	:	GRIFFITHSIA
	Organism Taxid	:	35158
	Synonym	:	GRFT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 10)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP
2	BGC	6	Ligand/Ion	BETA-D-GLUCOSE
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:108 , ASP A:109 , TYR A:110 , ASP A:112 , HOH A:447 , HOH A:450 , GLY B:11 , GLY B:12	BINDING SITE FOR RESIDUE BGC A 301
2	AC2	SOFTWARE	GLY A:26 , SER A:27 , TYR A:28 , ASP A:30 , GLY A:44 , HOH A:403 , HOH A:436 , HOH A:441 , HOH A:444 , HOH A:496 , HOH A:517	BINDING SITE FOR RESIDUE BGC A 302
3	AC3	SOFTWARE	GLY A:66 , ASP A:67 , TYR A:68 , ASP A:70 , GLY A:89 , GLY A:90 , HOH A:470	BINDING SITE FOR RESIDUE BGC A 303
4	AC4	SOFTWARE	GLY A:11 , GLY A:12 , ASN A:45 , EDO A:402 , GLY B:108 , ASP B:109 , TYR B:110 , ASP B:112 , HOH B:345 , HOH B:362 , HOH B:381 , HOH B:414	BINDING SITE FOR RESIDUE BGC B 304
5	AC5	SOFTWARE	GLY B:26 , SER B:27 , TYR B:28 , ASP B:30 , GLY B:44 , HOH B:337 , HOH B:391 , HOH B:397 , HOH B:429	BINDING SITE FOR RESIDUE BGC B 305
6	AC6	SOFTWARE	ARG A:64 , ALA A:92 , HOH A:504 , GLY B:66 , ASP B:67 , TYR B:68 , ASP B:70 , GLY B:90 , HOH B:331 , HOH B:372 , HOH B:403	BINDING SITE FOR RESIDUE BGC B 306
7	AC7	SOFTWARE	ASN A:93 , THR A:94 , HOH A:530 , HOH A:537 , SER B:96 , ASN B:97 , HOH B:375 , HOH B:386	BINDING SITE FOR RESIDUE SO4 A 401
8	AC8	SOFTWARE	GLY A:12 , SER A:13 , ARG A:24 , ASN A:45 , LEU A:46 , BGC B:304	BINDING SITE FOR RESIDUE EDO A 402

(no "SS Bond" information available for 2NUO)

Asymmetric/Biological Unit

No.	Residues
1	Gly A:83	-	Pro A:84
2	Gly B:83	-	Pro B:84

(no "SAP(SNP)/Variant" information available for 2NUO)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	JACALIN_LECTIN	PS51752	Jacalin-type lectin domain profile.	GRFIN_GRISQ	1-120	2	A:1-120 B:1-120

(no "Exon" information available for 2NUO)

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
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Chain A from PDB  Type:PROTEIN  Length:122
 aligned with GRFIN_GRISQ | P84801 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:122
                             1                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119  
          GRFIN_GRISQ     - -SLTHRKFGGSGGSPFSGLSSIAVRSGSYLDXIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
               SCOP domains -d2nuoa1 A:1-121 Griffithsin                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....eee....eeeeee...eeeeee..eeee....ee...ee......eeeeeeee...eeeeeeee....eeeeee....eeeeee.eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -JACALIN_LECTIN  PDB: A:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nuo A   0 xSLTHRKFGGSGGSPFSGLSSIAVRSGSYLDAIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
                            |        9        19        29        39        49        59        69        79        89        99       109       119  
                            |                                                                                                                         
                            0-ACE

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with GRFIN_GRISQ | P84801 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:122
                             1                                                                                                                        
                             |       9        19        29        39        49        59        69        79        89        99       109       119  
          GRFIN_GRISQ     - -SLTHRKFGGSGGSPFSGLSSIAVRSGSYLDXIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
               SCOP domains -d2nuob1 B:1-121 Griffithsin                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------Jacalin-2nuoB01 B:13-120                                                                                    - Pfam domains (1)
           Pfam domains (2) -------------Jacalin-2nuoB02 B:13-120                                                                                    - Pfam domains (2)
         Sec.struct. author .eeeeeeee....eee....eeeeee...eeeeee..eeee....ee...ee......eeeeeeee...eeeeeeee....eeeeee....eeeeee.eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -JACALIN_LECTIN  PDB: B:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nuo B   0 xSLTHRKFGGSGGSPFSGLSSIAVRSGSYLDAIIIDGVHHGGSGGNLSPTFTFGSGEYISNMTIRSGDYIDNISFETNMGRRFGPYGGSGGSANTLSNVKVIQINGSAGDYLDSLDIYYEQY 121
                            |        9        19        29        39        49        59        69        79        89        99       109       119  
                            0-ACE

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: beta-Prism I (50)

Superfamily: Mannose-binding lectins (42)

Family: Mannose-binding lectins (32)

Protein domain: Griffithsin (8)

Griffithsia sp. Q66D336 [TaxId: 373036] (1)

1a	d2nuoa1	A:1-121
1b	d2nuob1	B:1-121

(no "CATH Domain" information available for 2NUO)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Jacalin] (35)

Family: Jacalin (35)

Griffithsia sp. (strain Q66D336) (Red alga) (6)

1a	Jacalin-2nuoB01	B:13-120
1b	Jacalin-2nuoB02	B:13-120

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (GRFIN_GRISQ | P84801)

molecular function
	GO:0046871	N-acetylgalactosamine binding	Interacting selectively and non-covalently with N-acetylgalactosamine, 2-acetamido-2-deoxygalactopyranose, the n-acetyl derivative of galactosamine.
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0005536	glucose binding	Interacting selectively and non-covalently with the D- or L-enantiomer of glucose.
	GO:0005537	mannose binding	Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0008150	biological_process	Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end.
cellular component
	GO:0005623	cell	The basic structural and functional unit of all organisms. Includes the plasma membrane and any external encapsulating structures such as the cell wall and cell envelope.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Gly A:83 - Pro A:84	[ RasMol ]
		Gly B:83 - Pro B:84	[ RasMol ]

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	GRFIN_GRISQ \| P84801	:	2gty 2guc 2gud 2gue 2gux 2hyq 2hyr 2nu5 3lky 3ll0 3ll1 3ll2

2gty	CRYSTAL STRUCTURE OF UNLIGANDED GRIFFITHSIN
2guc	CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MANNOSE AT 1.78 A RESOLUTION
2gud	CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MANNOSE AT 0.94 A RESOLUTION
2gue	CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH N- ACETYLGLUCOSAMINE
2gux	SELENOMETHIONINE DERIVATIVE OF GRIFFITHSIN
2hyq	CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH 6ALPHA- MANNOBIOSE
2hyr	CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MALTOSE
2i43	THEORETICAL MODEL OF A COMPLEX OF GRIFFITHSIN WITH MAN9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 10)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

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