4YM0 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE HUMAN GALECTIN-4 C-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN IN COMPLEX WITH LACTO-N-TETRAOSE (LNT)

Authors :   K. Bum-Erdene, H. Blanchard

Date :   06 Mar 15 (Deposition) - 01 Jul 15 (Release) - 09 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: D  (1x)
Biol. Unit 4: C  (1x)

Keywords :   Galectin, Lectin, Carbohydrate Binding Protein, Lacto-N-Tetraose, Carbohydrate Recognition, Beta Sandwich, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Bum-Erdene, H. Leffler, U. J. Nilsson, H. Blanchard
Structural Characterization Of Human Galectin-4 C-Terminal Domain: Elucidating The Molecular Basis For Recognition Of Glycosphingolipids, Sulfated Saccharides And Blood Group Antigens.
Febs J. V. 282 3348 2015
PubMed-ID: 26077389 | Reference-DOI: 10.1111/FEBS.13348

Molecule 1 - GALECTIN-4
	Chains	:	A, B, D, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 171-323
	Gene	:	LGALS4
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GAL-4,ANTIGEN NY-CO-27,L-36 LACTOSE-BINDING PROTEIN,L36LBP, LACTOSE-BINDING LECTIN 4

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	LAT	3	Ligand/Ion	BETA-LACTOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	1	Ligand/Ion	GLYCEROL
3	LAT	1	Ligand/Ion	BETA-LACTOSE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	LAT	1	Ligand/Ion	BETA-LACTOSE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	LAT	-1	Ligand/Ion	BETA-LACTOSE
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 4 (1, 1)

No.	Name	Count	Type	Full Name
1	GAL	-1	Ligand/Ion	BETA-D-GALACTOSE
2	GOL	-1	Ligand/Ion	GLYCEROL
3	LAT	1	Ligand/Ion	BETA-LACTOSE
4	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:279 , GLY A:281 , LEU A:282 , ASP A:283 , ARG A:284 , LYS A:286	binding site for residue GOL A 404
2	AC2	SOFTWARE	LEU B:252 , ASN B:253 , SER B:255 , SER B:302 , HIS C:236 , ASN C:238 , ARG C:240 , VAL C:247 , ASN C:249 , TRP C:256 , GLU C:259	binding site for residue LAT C 401
3	AC3	SOFTWARE	ALA A:222 , ASN A:224 , HIS A:236 , ASN A:238 , ARG A:240 , ASN A:249 , TRP A:256 , GLU A:259 , GLN A:313 , HOH A:509 , HOH A:518	binding site for Poly-Saccharide residues LAT A 401 through GAL A 403
4	AC4	SOFTWARE	ALA A:222 , ASN A:224 , HIS A:236 , ASN A:238 , ARG A:240 , ASN A:249 , TRP A:256 , GLU A:259 , GLN A:313 , HOH A:509 , HOH A:518 , ASN B:224 , HIS B:236 , ASN B:238 , ARG B:240 , ASN B:249 , GLU B:259 , GLN B:313 , HOH B:510 , HOH B:521	binding site for Poly-Saccharide residues LAT B 401 through GAL B 403
5	AC5	SOFTWARE	LEU A:252 , ASN A:253 , SER A:255 , ASN B:224 , HIS B:236 , ASN B:238 , ARG B:240 , ASN B:249 , GLU B:259 , GLN B:313 , HOH B:510 , HOH B:521 , HIS D:236 , ASN D:238 , ARG D:240 , ASN D:249 , GLU D:259 , HOH D:501 , HOH D:511	binding site for Poly-Saccharide residues GAL D 401 through NAG D 402

(no "SS Bond" information available for 4YM0)

Asymmetric Unit

No.	Residues
1	Val A:192	-	Pro A:193
2	Val B:192	-	Pro B:193
3	Val D:192	-	Pro D:193
4	Val C:192	-	Pro C:193

(no "SAP(SNP)/Variant" information available for 4YM0)

(no "PROSITE Motif" information available for 4YM0)

(no "Exon" information available for 4YM0)

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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeee.........eeeeeee.......eeeeee......eeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee..........eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ym0 A 186 PTFNPPVPYFGRLQGGLTARRTIIIKGYVPPTGKSFAINFKVGSSGDIALHINPRMGNGTVVRNSLLNGSWGSEEKKITHNPFGPGQFFDLSIRCGLDRFKVYANGQHLFDFAHRLSAFQRVDTLEIQGDVTLSYVQI 323
                                   195       205       215       225       235       245       255       265       275       285       295       305       315

Chain B from PDB  Type:PROTEIN  Length:139
                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.........eeeeeee.......eeeeee......eeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee..hhhhh...eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ym0 B 185 PPTFNPPVPYFGRLQGGLTARRTIIIKGYVPPTGKSFAINFKVGSSGDIALHINPRMGNGTVVRNSLLNGSWGSEEKKITHNPFGPGQFFDLSIRCGLDRFKVYANGQHLFDFAHRLSAFQRVDTLEIQGDVTLSYVQI 323
                                   194       204       214       224       234       244       254       264       274       284       294       304       314

Chain C from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeee.........eeeeeee.......eeeeee......eeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee....hhhhh.eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ym0 C 184 GPPTFNPPVPYFGRLQGGLTARRTIIIKGYVPPTGKSFAINFKVGSSGDIALHINPRMGNGTVVRNSLLNGSWGSEEKKITHNPFGPGQFFDLSIRCGLDRFKVYANGQHLFDFAHRLSAFQRVDTLEIQGDVTLSYVQI 323
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323

Chain D from PDB  Type:PROTEIN  Length:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.....eeee........eeeeeeee.......eeeeeee....eeeeeeeee....eeeeeeee..ee................eeeeeeee...eeeeee..eeeeeee..........eeeeee..eeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ym0 D 184 GPPTFNPPVPYFGRLQGGLTARRTIIIKGYVPPTGKSFAINFKVGSSGDIALHINPRMGNGTVVRNSLLNGSWGSEEKKITHNPFGPGQFFDLSIRCGLDRFKVYANGQHLFDFAHRLSAFQRVDTLEIQGDVTLSYVQI 323
                                   193       203       213       223       233       243       253       263       273       283       293       303       313       323

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 '\|'

(no "SCOP Domain" information available for 4YM0)

(no "CATH Domain" information available for 4YM0)

(no "Pfam Domain" information available for 4YM0)

Asymmetric Unit(hide GO term definitions)

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		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:192 - Pro A:193	[ RasMol ]
		Val B:192 - Pro B:193	[ RasMol ]
		Val C:192 - Pro C:193	[ RasMol ]
		Val D:192 - Pro D:193	[ RasMol ]

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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

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	LEG4_HUMAN \| P56470	:	1x50 4xzp 4ylz 4ym1 4ym2 4ym3 5cbl 5duu 5duv 5duw 5dux

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Ligands, Modified Residues, Ions (4, 10)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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