2HYR - JenaLib

Title :   CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH MALTOSE

Authors :   N. E. Ziolkowska, A. Wlodawer

Date :   07 Aug 06 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.51

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, J. B. Mcmahon, K. E. Palmer, R. A. Dwek, M. R. Wormald, A. Wlodawer
Crystallographic, Thermodynamic, And Molecular Modeling Studies Of The Mode Of Binding Of Oligosaccharides To The Potent Antiviral Protein Griffithsin.
Proteins V. 67 661 2007
PubMed-ID: 17340634 | Reference-DOI: 10.1002/PROT.21336

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 22)

Sites (20, 20)

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:109 , GLC A:123 , SO4 A:401 , HOH A:717	BINDING SITE FOR RESIDUE BGC A 122
02	AC2	SOFTWARE	GLY A:108 , ASP A:109 , TYR A:110 , ASP A:112 , BGC A:122 , HOH A:661 , HOH A:704 , HOH A:720 , GLY B:11 , GLY B:12 , GLN B:120	BINDING SITE FOR RESIDUE GLC A 123
03	AC3	SOFTWARE	SER A:27 , GLC A:125 , HOH A:647 , GLY B:66 , GLY B:90 , SER B:91 , GLC B:127 , HOH B:715	BINDING SITE FOR RESIDUE BGC A 124
04	AC4	SOFTWARE	GLY A:26 , SER A:27 , TYR A:28 , ASP A:30 , GLY A:43 , GLY A:44 , TYR A:110 , BGC A:124 , HOH A:663 , HOH A:733 , BGC B:122 , HOH B:707	BINDING SITE FOR RESIDUE GLC A 125
05	AC5	SOFTWARE	TYR A:28 , ASP A:67 , GLC A:127 , HOH A:726 , BGC B:126	BINDING SITE FOR RESIDUE BGC A 126
06	AC6	SOFTWARE	GLY A:66 , ASP A:67 , TYR A:68 , ASP A:70 , GLY A:89 , GLY A:90 , BGC A:126 , HOH A:698 , HOH A:752 , BGC B:124	BINDING SITE FOR RESIDUE GLC A 127
07	AC7	SOFTWARE	ASN A:93 , THR A:94 , BGC A:122 , HOH A:680 , HOH A:688 , HOH A:701 , HOH A:703 , HOH A:706 , ASN B:97 , HOH B:669	BINDING SITE FOR RESIDUE SO4 A 401
08	AC8	SOFTWARE	ARG A:64 , SER A:91 , ALA A:92 , HOH A:662	BINDING SITE FOR RESIDUE SO4 A 402
09	AC9	SOFTWARE	HOH A:636 , HOH A:704 , HOH A:706 , HOH A:707 , HOH A:708 , HOH A:717	BINDING SITE FOR RESIDUE MG A 501
10	BC1	SOFTWARE	HOH A:692 , HOH A:736 , HOH A:737 , HOH A:738 , HOH A:740 , HOH B:711	BINDING SITE FOR RESIDUE MG A 502
11	BC2	SOFTWARE	GLY A:17 , LEU A:18 , ILE A:34 , ASP A:35 , GLN A:102 , GLY B:17 , LEU B:18 , ILE B:34 , ASP B:35 , GLN B:102	BINDING SITE FOR RESIDUE EDO A 601
12	BC3	SOFTWARE	THR A:49 , PHE A:50 , THR A:51 , ARG A:80 , HOH A:637 , HOH A:724 , HOH B:604	BINDING SITE FOR RESIDUE EDO A 603
13	BC4	SOFTWARE	GLC A:125 , HOH A:741 , ASP B:109 , GLC B:123 , HOH B:724	BINDING SITE FOR RESIDUE BGC B 122
14	BC5	SOFTWARE	GLY A:11 , GLY A:12 , ASN A:45 , GLY B:108 , ASP B:109 , TYR B:110 , ASP B:112 , BGC B:122 , HOH B:668 , HOH B:701 , HOH B:707	BINDING SITE FOR RESIDUE GLC B 123
15	BC6	SOFTWARE	GLC A:127 , HOH A:752 , SER B:27 , GLC B:125 , HOH B:680	BINDING SITE FOR RESIDUE BGC B 124
16	BC7	SOFTWARE	GLY B:26 , SER B:27 , TYR B:28 , ASP B:30 , GLY B:44 , BGC B:124 , HOH B:673	BINDING SITE FOR RESIDUE GLC B 125
17	BC8	SOFTWARE	BGC A:126 , TYR B:28 , ASP B:67 , TYR B:68 , GLC B:127 , HOH B:661	BINDING SITE FOR RESIDUE BGC B 126
18	BC9	SOFTWARE	BGC A:124 , HOH A:726 , TYR B:28 , GLY B:66 , ASP B:67 , TYR B:68 , ASP B:70 , GLY B:89 , GLY B:90 , BGC B:126 , HOH B:637 , HOH B:643 , HOH B:655	BINDING SITE FOR RESIDUE GLC B 127
19	CC1	SOFTWARE	ARG B:64 , SER B:91 , ALA B:92	BINDING SITE FOR RESIDUE SO4 B 403
20	CC2	SOFTWARE	HOH A:666 , ARG B:5 , LYS B:6 , SER B:59 , ASN B:60 , GLU B:75 , THR B:76 , ASN B:77	BINDING SITE FOR RESIDUE EDO B 602

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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: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 -d2hyra1 A:1-121 Griffithsin                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....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
                 2hyr 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 -d2hyrb1 B:1-121 Griffithsin                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         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
                 2hyr 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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

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.

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