3B9C - JenaLib

Asymmetric Unit (Jmol Viewer)

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 HUMAN GRP CRD

Authors :   D. Zhou, H. H. Ge, L. W. Niu, M. K. Teng

Date :   05 Nov 07 (Deposition) - 18 Mar 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Beta Sandwich, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Zhou, H. Ge, J. Sun, Y. Gao, M. Teng, L. Niu
Crystal Structure Of The C-Terminal Conserved Domain Of Human Grp, A Galectin-Related Protein, Reveals A Function Mode Different From Those Of Galectins.
Proteins V. 71 1582 2008
PubMed-ID: 18320588 | Reference-DOI: 10.1002/PROT.22003
(for further references see the PDB file header)

Molecule 1 - HSPC159
	Chains	:	A, D, C, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	P28
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 38-172
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B	C	D
Biological Unit 2 (1x)	:	A	B
Biological Unit 3 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 13)

No.	Name	Count	Type	Full Name
1	BME	6	Ligand/Ion	BETA-MERCAPTOETHANOL
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 13)

No.	Name	Count	Type	Full Name
1	BME	6	Ligand/Ion	BETA-MERCAPTOETHANOL
2	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	BME	2	Ligand/Ion	BETA-MERCAPTOETHANOL
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 7)

No.	Name	Count	Type	Full Name
1	BME	4	Ligand/Ion	BETA-MERCAPTOETHANOL
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:74 , SER A:75 , ALA A:76 , HOH A:175 , THR B:56	BINDING SITE FOR RESIDUE SO4 A 137
02	AC2	SOFTWARE	ARG A:58 , TYR A:79 , PHE A:80 , HOH A:151 , ARG B:58 , TYR B:79 , PHE B:80	BINDING SITE FOR RESIDUE SO4 A 138
03	AC3	SOFTWARE	THR C:56 , ARG D:62 , GLN D:74 , SER D:75 , ALA D:76 , HOH D:194	BINDING SITE FOR RESIDUE SO4 D 137
04	AC4	SOFTWARE	ARG C:58 , TYR C:79 , PHE C:80 , ARG D:58 , TYR D:79 , PHE D:80 , HOH D:152 , HOH D:191	BINDING SITE FOR RESIDUE SO4 D 138
05	AC5	SOFTWARE	ARG C:62 , GLN C:74 , SER C:75 , ALA C:76 , HOH C:222 , HOH C:237 , THR D:56	BINDING SITE FOR RESIDUE SO4 C 137
06	AC6	SOFTWARE	THR A:56 , ARG B:62 , GLN B:74 , SER B:75 , ALA B:76 , HOH B:175 , HOH B:180	BINDING SITE FOR RESIDUE SO4 B 137
07	AC7	SOFTWARE	ARG B:98 , ARG B:100 , HOH B:160 , HOH B:188 , HOH B:204 , ARG D:98 , ARG D:100	BINDING SITE FOR RESIDUE SO4 B 138
08	AC8	SOFTWARE	GLY A:38 , ALA A:120 , HOH A:241 , BME B:139	BINDING SITE FOR RESIDUE BME A 139
09	AC9	SOFTWARE	LYS D:17 , HOH D:172	BINDING SITE FOR RESIDUE BME D 139
10	BC1	SOFTWARE	BME C:138 , CYS D:37 , ALA D:120 , HOH D:219	BINDING SITE FOR RESIDUE BME D 140
11	BC2	SOFTWARE	ALA C:120 , ASP C:122 , BME D:140	BINDING SITE FOR RESIDUE BME C 138
12	BC3	SOFTWARE	TYR C:96 , GLN C:116 , HOH C:178 , HOH C:238	BINDING SITE FOR RESIDUE BME C 139
13	BC4	SOFTWARE	BME A:139 , HOH A:241 , ALA B:120 , ASP B:122 , HOH B:181	BINDING SITE FOR RESIDUE BME B 139

(no "SS Bond" information available for 3B9C)

Asymmetric Unit

No.	Residues
1	Asp A:42	-	Pro A:43
2	Asp D:42	-	Pro D:43
3	Asp C:42	-	Pro C:43
4	Asp B:42	-	Pro B:43

(no "SAP(SNP)/Variant" information available for 3B9C)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEGL_HUMAN	40-172	4	A:4-136 B:4-136 C:4-136 D:4-136

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEGL_HUMAN	40-172	4	A:4-136 B:4-136 C:4-136 D:4-136

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEGL_HUMAN	40-172	2	A:4-136 B:4-136 - -

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	GALECTIN	PS51304	Galactoside-binding lectin (galectin) domain profile.	LEGL_HUMAN	40-172	2	- - C:4-136 D:4-136

(no "Exon" information available for 3B9C)

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:134
 aligned with LEGL_HUMAN | Q3ZCW2 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:134
                                    48        58        68        78        88        98       108       118       128       138       148       158       168    
           LEGL_HUMAN    39 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 172
               SCOP domains d3b9ca_ A: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeeeee.....eeeeeeee........eeeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GALECTIN  PDB: A:4-136 UniProt: 40-172                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b9c A   3 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEYPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with LEGL_HUMAN | Q3ZCW2 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:134
                                    48        58        68        78        88        98       108       118       128       138       148       158       168    
           LEGL_HUMAN    39 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 172
               SCOP domains d3b9cb_ B: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeeeee.....eeeeeee..........eeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GALECTIN  PDB: B:4-136 UniProt: 40-172                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b9c B   3 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEYPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain C from PDB  Type:PROTEIN  Length:134
 aligned with LEGL_HUMAN | Q3ZCW2 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:134
                                    48        58        68        78        88        98       108       118       128       138       148       158       168    
           LEGL_HUMAN    39 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 172
               SCOP domains d3b9cc_ C: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeeeee.....eeeeeeee........eeeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GALECTIN  PDB: C:4-136 UniProt: 40-172                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b9c C   3 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEYPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with LEGL_HUMAN | Q3ZCW2 from UniProtKB/Swiss-Prot  Length:172

    Alignment length:134
                                    48        58        68        78        88        98       108       118       128       138       148       158       168    
           LEGL_HUMAN    39 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEHPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 172
               SCOP domains d3b9cd_ D: automated matches                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.........eeeeeeee.....eeeeeeee........eeeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee.eeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -GALECTIN  PDB: D:4-136 UniProt: 40-172                                                                                                PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b9c D   3 PFCGHIKGGMRPGKKVLVMGIVDLNPESFAISLTCGDSEDPPADVAIELKAVFTDRQLLRNSCISGERGEEQSAIPYFPFIPDQPFRVEILCEYPRFRVFVDGHQLFDFYHRIQTLSAIDTIKINGDLQITKLG 136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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: Concanavalin A-like lectins/glucanases (797)

Superfamily: Concanavalin A-like lectins/glucanases (797)

Family: automated matches (133)

Protein domain: automated matches (133)

Human (Homo sapiens) [TaxId: 9606] (36)

1a	d3b9ca_	A:
1b	d3b9cb_	B:
1c	d3b9cc_	C:
1d	d3b9cd_	D:

(no "CATH Domain" information available for 3B9C)

(no "Pfam Domain" information available for 3B9C)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (LEGL_HUMAN | Q3ZCW2)

molecular function
	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: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).
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

Asymmetric Unit
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	Cis Peptide Bonds
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		Asp D:42 - Pro D:43	[ RasMol ]

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	3b9c
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(no "Related Entries Specified in the PDB File" available for 3B9C)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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