2GUE - JenaLib

Title :   CRYSTAL STRUCTURE OF A COMPLEX OF GRIFFITHSIN WITH N-ACETYLGLUCOSAMINE

Authors :   N. E. Ziolkowska, A. Wlodawer

Date :   29 Apr 06 (Deposition) - 01 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.02

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, B. R. O'Keefe, T. Mori, C. Zhu, B. Giomarelli, F. Vojdani, K. E. Palmer, J. B. Mcmahon, A. Wlodawer
Domain-Swapped Structure Of The Potent Antiviral Protein Griffithsin And Its Mode Of Carbohydrate Binding.
Structure V. 14 1127 2006
PubMed-ID: 16843894 | Reference-DOI: 10.1016/J.STR.2006.05.017

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 29)

Sites (27, 27)

Asymmetric Unit (27, 27)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR B:28 , GLY B:66 , ASP B:67 , TYR B:68 , ASP B:70 , GLU B:75 , ARG B:81 , GLY B:89 , GLY B:90	BINDING SITE FOR RESIDUE NAG B 122
02	AC2	SOFTWARE	TYR B:68 , GLY B:108 , ASP B:109 , TYR B:110 , ASP B:112	BINDING SITE FOR RESIDUE SO4 B 201
03	AC3	SOFTWARE	TYR A:68 , GLY A:108 , ASP A:109 , TYR A:110 , ASP A:112	BINDING SITE FOR RESIDUE SO4 A 202
04	AC4	SOFTWARE	SER A:27 , GLY A:87 , SER A:88 , LYS B:99 , TYR B:121 , HOH B:340	BINDING SITE FOR RESIDUE SO4 B 203
05	AC5	SOFTWARE	HIS A:4 , LYS A:6 , ARG B:80 , HOH B:374	BINDING SITE FOR RESIDUE SO4 A 204
06	AC6	SOFTWARE	ARG B:64 , ARG B:81 , ALA B:92 , HOH B:343	BINDING SITE FOR RESIDUE SO4 B 205
07	AC7	SOFTWARE	SER B:16 , LEU B:18 , GLU B:56 , TYR B:57 , ILE B:58 , VAL B:100	BINDING SITE FOR RESIDUE EDO B 301
08	AC8	SOFTWARE	GLY A:17 , LEU A:18 , ASP A:35 , GLN A:102 , GLY B:17 , LEU B:18 , ASP B:35 , GLN B:102	BINDING SITE FOR RESIDUE EDO A 302
09	AC9	SOFTWARE	ASN A:60 , MET A:61 , THR A:62 , SER A:73 , PHE A:74 , THR A:94	BINDING SITE FOR RESIDUE EDO A 303
10	BC1	SOFTWARE	SER A:16 , LEU A:18 , PHE A:52 , GLU A:56 , TYR A:57 , ILE A:58 , VAL A:100 , HOH A:356	BINDING SITE FOR RESIDUE EDO A 304
11	BC2	SOFTWARE	ASN A:104 , ASP A:115 , TYR A:117 , EDO A:307	BINDING SITE FOR RESIDUE EDO A 305
12	BC3	SOFTWARE	SER A:65 , GLY A:66 , HOH A:366 , PHE B:7 , GLY B:8 , HOH B:371	BINDING SITE FOR RESIDUE EDO B 306
13	BC4	SOFTWARE	GLY A:105 , SER A:106 , SER A:113 , EDO A:305 , HOH A:377 , LYS B:6 , PHE B:15	BINDING SITE FOR RESIDUE EDO A 307
14	BC5	SOFTWARE	PRO A:14 , ALA A:22 , LEU A:46 , SER A:47 , PRO A:48 , THR A:49 , HOH A:324 , HOH A:328	BINDING SITE FOR RESIDUE EDO A 308
15	BC6	SOFTWARE	ARG A:81 , HOH A:345 , HOH A:378 , ARG B:24 , HIS B:38 , LEU B:46 , HOH B:325 , HOH B:370	BINDING SITE FOR RESIDUE EDO B 309
16	BC7	SOFTWARE	PHE A:50 , THR A:51 , GLY A:53 , GLU A:56 , ARG A:80 , HOH A:332	BINDING SITE FOR RESIDUE EDO A 310
17	BC8	SOFTWARE	SER A:25 , GLY A:26 , TYR A:85 , GLY A:86 , EDO A:315 , HOH A:350 , HOH A:372 , HOH A:379	BINDING SITE FOR RESIDUE EDO A 311
18	BC9	SOFTWARE	LEU A:46 , PRO A:48 , TYR A:85 , EDO A:315 , EDO B:321	BINDING SITE FOR RESIDUE EDO A 312
19	CC1	SOFTWARE	SER B:59 , ASN B:60 , SER B:96 , ASN B:97 , HOH B:375	BINDING SITE FOR RESIDUE EDO B 313
20	CC2	SOFTWARE	ASN A:93 , THR A:94	BINDING SITE FOR RESIDUE EDO A 314
21	CC3	SOFTWARE	VAL A:23 , SER A:25 , ASN A:45 , SER A:47 , TYR A:85 , EDO A:311 , EDO A:312 , HOH A:350	BINDING SITE FOR RESIDUE EDO A 315
22	CC4	SOFTWARE	PHE A:15 , SER A:16 , SER A:19 , HOH A:371 , HOH A:384 , HIS B:39	BINDING SITE FOR RESIDUE EDO A 316
23	CC5	SOFTWARE	SER B:27 , TYR B:28 , ASP B:30	BINDING SITE FOR RESIDUE EDO B 317
24	CC6	SOFTWARE	THR B:62 , ARG B:64 , ASN B:71 , ILE B:72 , SER B:73	BINDING SITE FOR RESIDUE EDO B 318
25	CC7	SOFTWARE	PHE A:15 , ASN B:104 , GLY B:105 , ASP B:115 , TYR B:117	BINDING SITE FOR RESIDUE EDO B 319
26	CC8	SOFTWARE	THR A:62 , SER A:73 , PRO A:84 , HOH A:330 , HOH A:361	BINDING SITE FOR RESIDUE EDO A 320
27	CC9	SOFTWARE	EDO A:312 , ARG B:24 , ASN B:45 , LEU B:46	BINDING SITE FOR RESIDUE EDO B 321

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 -d2guea1 A: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: A:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gue 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 -d2gueb1 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....eeeee..eeeeeeeeee...eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -JACALIN_LECTIN  PDB: B:1-120 UniProt: 1-120                                                                             - PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gue 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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