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Asym./Biol. Unit (Jmol Viewer)

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Title :   PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH LACTO-N-NEO-FUCOPENTAOSE V(LNPFV)

Authors :   S. Perret, C. Sabin, C. Dumon, M. Budova, C. Gautier, O. Galanina, S. Ilia, N. Bovin, M. Nicaise, M. Desmadril, N. Gilboa-Garber, M. Wimmerova, E. P. Mitchell, A. Imberty

Date :   21 Sep 04 (Deposition) - 31 Mar 05 (Release) - 30 Jan 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.05

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

Keywords :   Sugar Binding Protein, Pentassacharide, Cystic Firosis Infection Of Lungs (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Perret, C. Sabin, C. Dumon, M. Pokorna, C. Gautier, O. Galanina, S. Ilia, N. Bovin, M. Nicaise, M. Desmadril, N. Gilboa-Garber, M. Wimmerova, E. P. Mitchell, A. Imberty
Structural Basis For The Interaction Between Human Milk Oligosaccharides And The Bacterial Lectin Pa-Iil Of Pseudomonas Aeruginosa.
Biochem. J. V. 389 325 2005
PubMed-ID: 15790314 | Reference-DOI: 10.1042/BJ20050079
(for further references see the PDB file header)

Molecule 1 - PSEUDOMONAS AERUGINOSA LECTIN II
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET25PA2L
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287
	Other Details	:	EACH MONOMER CONTAINS TWO CLOSE CALCIUM CATIONS THAT MEDIATE THE BINDING OF THE SACCHARIDE
	Synonym	:	PA-IIL

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (7, 31)

No.	Name	Count	Type	Full Name
1	BGC	4	Ligand/Ion	BETA-D-GLUCOSE
2	CA	8	Ligand/Ion	CALCIUM ION
3	FUC	4	Ligand/Ion	ALPHA-L-FUCOSE
4	GAL	6	Ligand/Ion	BETA-D-GALACTOSE
5	GOL	2	Ligand/Ion	GLYCEROL
6	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
7	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (31, 31)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:21 , SER A:22 , SER A:23 , GLU A:95 , ASP A:96 , ASP A:99 , ASP A:101 , ASP A:104 , CA A:1116 , CA A:1117 , BGC A:1119 , GAL A:1120 , HOH A:2157 , GLY C:114	BINDING SITE FOR RESIDUE SO4 A1115
02	AC2	SOFTWARE	SER A:23 , ASP A:96 , FUC A:1118 , GAL A:1120 , HOH A:2152 , HOH A:2154 , HOH A:2155 , HOH A:2156	BINDING SITE FOR RESIDUE CA A1116
03	AC3	SOFTWARE	ASP A:99 , FUC A:1118 , BGC A:1119 , NAG A:1121 , HOH A:2157 , HOH A:2158 , HOH A:2159 , HOH A:2160 , HOH A:2161	BINDING SITE FOR RESIDUE CA A1117
04	AC4	SOFTWARE	GAL A:1120 , HOH A:2162 , HOH A:2163 , HOH A:2164 , HOH A:2166 , GLU D:35 , HOH D:2063	BINDING SITE FOR RESIDUE SO4 B1115
05	AC5	SOFTWARE	ASN B:21 , SER B:22 , SER B:23 , GLU B:95 , ASP B:96 , ASP B:99 , ASP B:101 , ASP B:104 , CA B:1116 , CA B:1117 , BGC B:1119 , GAL B:1120 , HOH B:2186 , GLY D:114	BINDING SITE FOR RESIDUE CA B1116
06	AC6	SOFTWARE	SER B:23 , ASP B:96 , FUC B:1118 , GAL B:1120 , HOH B:2177 , HOH B:2178 , HOH B:2179 , HOH B:2180 , HOH B:2181 , HOH B:2182 , HOH B:2183	BINDING SITE FOR RESIDUE CA B1117
07	AC7	SOFTWARE	THR B:98 , ASP B:99 , FUC B:1118 , BGC B:1119 , NAG B:1121 , GOL B:1123 , HOH B:2163 , HOH B:2184 , HOH B:2185 , HOH B:2186 , HOH B:2187	BINDING SITE FOR RESIDUE SO4 C1115
08	AC8	SOFTWARE	GAL B:1120 , GAL B:1122 , HOH B:2187 , HOH B:2188 , HOH B:2189 , HOH B:2191 , HOH B:2192 , HOH B:2195 , GAL D:1122	BINDING SITE FOR RESIDUE CA C1116
09	AC9	SOFTWARE	NAG B:1121 , HOH B:2031 , HOH B:2194 , HOH B:2195 , HOH B:2196 , HOH B:2197 , NAG D:1121 , GAL D:1122 , HOH D:2170	BINDING SITE FOR RESIDUE CA C1117
10	BC1	SOFTWARE	GLY A:114 , ASN C:21 , SER C:22 , SER C:23 , GLU C:95 , ASP C:96 , ASP C:99 , ASP C:101 , ASP C:104 , CA C:1116 , CA C:1117 , BGC C:1119 , GAL C:1120 , HOH C:2182	BINDING SITE FOR RESIDUE SO4 D1115
11	BC2	SOFTWARE	SER C:23 , ASP C:96 , FUC C:1118 , GAL C:1120 , HOH C:2177 , HOH C:2178	BINDING SITE FOR RESIDUE CA D1116
12	BC3	SOFTWARE	ASP C:99 , FUC C:1118 , BGC C:1119 , HOH C:2182 , HOH C:2183 , HOH C:2185 , HOH C:2187	BINDING SITE FOR RESIDUE CA D1117
13	BC4	SOFTWARE	GLY B:114 , ASN D:21 , SER D:22 , SER D:23 , GLU D:95 , ASP D:96 , ASP D:99 , ASP D:101 , ASP D:104 , CA D:1116 , CA D:1117 , BGC D:1119 , GAL D:1120 , HOH D:2157	BINDING SITE FOR RESIDUE GOL B1123
14	BC5	SOFTWARE	SER D:23 , ASP D:96 , FUC D:1118 , GAL D:1120 , HOH D:2149 , HOH D:2150 , HOH D:2151 , HOH D:2153 , HOH D:2154	BINDING SITE FOR RESIDUE GOL D1123
15	BC6	SOFTWARE	THR D:98 , ASP D:99 , FUC D:1118 , BGC D:1119 , NAG D:1121 , GOL D:1123 , HOH D:2155 , HOH D:2156 , HOH D:2157 , HOH D:2158 , HOH D:2161	BINDING SITE FOR RESIDUES FUC A1118 AND BGC A1119
16	BC7	SOFTWARE	GAL B:1122 , GAL D:1120 , GAL D:1122 , HOH D:2159 , HOH D:2160 , HOH D:2161 , HOH D:2162 , HOH D:2163 , HOH D:2166	BINDING SITE FOR RESIDUES BGC A1119 AND GAL A1120
17	BC8	SOFTWARE	NAG B:1121 , GAL B:1122 , HOH B:2198 , NAG D:1121 , HOH D:2023 , HOH D:2144 , HOH D:2165 , HOH D:2166 , HOH D:2167	BINDING SITE FOR RESIDUES GAL A1120 AND NAG A1121
18	BC9	SOFTWARE	SER A:44 , THR A:45 , ASN A:46 , HOH A:2076 , HOH A:2150 , HOH A:2151 , SER D:44 , ASN D:46 , ALA D:48 , HOH D:2146	BINDING SITE FOR RESIDUES FUC B1118 AND BGC B1119
19	CC1	SOFTWARE	GLU A:95 , ASP A:99 , ASP A:101 , ASP A:104 , FUC A:1118	BINDING SITE FOR RESIDUES BGC B1119 AND GAL B1120
20	CC2	SOFTWARE	ASN A:21 , ASP A:101 , ASN A:103 , ASP A:104 , FUC A:1118 , GLY C:114	BINDING SITE FOR RESIDUES GAL B1120 AND NAG B1121
21	CC3	SOFTWARE	SER B:44 , THR B:45 , ASN B:46 , HOH B:2173 , HOH B:2175 , HOH B:2176	BINDING SITE FOR RESIDUES NAG B1121 AND GAL B1122
22	CC4	SOFTWARE	GLU B:95 , ASP B:99 , ASP B:101 , ASP B:104 , FUC B:1118	BINDING SITE FOR RESIDUES FUC C1118 AND BGC C1119
23	CC5	SOFTWARE	ASN B:21 , ASP B:101 , ASN B:103 , ASP B:104 , FUC B:1118 , GLY D:114	BINDING SITE FOR RESIDUES BGC C1119 AND GAL C1120
24	CC6	SOFTWARE	SER C:44 , THR C:45 , ASN C:46 , HOH C:2173 , HOH C:2174	BINDING SITE FOR RESIDUES FUC D1118 AND BGC D1119
25	CC7	SOFTWARE	GLU C:95 , ASP C:99 , ASP C:101 , ASP C:104 , FUC C:1118	BINDING SITE FOR RESIDUES BGC D1119 AND GAL D1120
26	CC8	SOFTWARE	GLY A:114 , ASN C:21 , ASP C:101 , ASN C:103 , ASP C:104 , FUC C:1118	BINDING SITE FOR RESIDUES GAL D1120 AND NAG D1121
27	CC9	SOFTWARE	HOH B:2196 , ARG C:13 , GLN D:43 , THR D:45 , HOH D:2145 , HOH D:2146 , HOH D:2147 , HOH D:2148	BINDING SITE FOR RESIDUES NAG D1121 AND GAL D1122
28	DC1	not defined	GLU D:95 , ASP D:99 , ASP D:101 , ASP D:104 , FUC D:1118
29	DC2	not defined	GLY B:114 , ASN D:21 , ASP D:101 , ASN D:103 , ASP D:104 , FUC D:1118
30	DC3	not defined	ASP B:99 , GAL B:1120 , HOH B:2167 , HOH B:2198 , HOH B:2200 , HOH B:2201 , HOH B:2202 , GLY D:114
31	DC4	not defined	GLY B:114 , ASP D:99 , GAL D:1120 , HOH D:2139 , HOH D:2169 , HOH D:2170 , HOH D:2171

(no "SS Bond" information available for 1W8F)

Asymmetric/Biological Unit

No.	Residues
1	Trp A:111	-	Pro A:112
2	Trp B:111	-	Pro B:112
3	Trp C:111	-	Pro C:112
4	Trp D:111	-	Pro D:112

(no "SAP(SNP)/Variant" information available for 1W8F)

(no "PROSITE Motif" information available for 1W8F)

(no "Exon" information available for 1W8F)

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:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d1w8fa_ A: automated matches                                                                                       SCOP domains
               CATH domains 1w8fA00 A:1-114 Calcium-mediated lectin                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1w8f A   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d1w8fb_ B: automated matches                                                                                       SCOP domains
               CATH domains 1w8fB00 B:1-114 Calcium-mediated lectin                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1w8f B   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110

Chain C from PDB  Type:PROTEIN  Length:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d1w8fc_ C: automated matches                                                                                       SCOP domains
               CATH domains 1w8fC00 C:1-114 Calcium-mediated lectin                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1w8f C   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110

Chain D from PDB  Type:PROTEIN  Length:114
 aligned with Q9HYN5_PSEAE | Q9HYN5 from UniProtKB/TrEMBL  Length:115

    Alignment length:114
                                    11        21        31        41        51        61        71        81        91       101       111    
         Q9HYN5_PSEAE     2 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 115
               SCOP domains d1w8fd_ D: automated matches                                                                                       SCOP domains
               CATH domains 1w8fD00 D:1-114 Calcium-mediated lectin                                                                            CATH domains
           Pfam domains (1) -----PA-IIL-1w8fD01 D:6-113                                                                                      - Pfam domains (1)
           Pfam domains (2) -----PA-IIL-1w8fD02 D:6-113                                                                                      - Pfam domains (2)
           Pfam domains (3) -----PA-IIL-1w8fD03 D:6-113                                                                                      - Pfam domains (3)
           Pfam domains (4) -----PA-IIL-1w8fD04 D:6-113                                                                                      - Pfam domains (4)
         Sec.struct. author ....eee......eeeeeeee....eeeeeee..eeeeeeee...eeeeeeeeee......eeeeeeee.....eeeeeeeee...eeeeeeee.........eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------ Transcript
                 1w8f D   1 ATQGVFTLPANTRFGVTAFANSSGTQTVNVLVNNETAATFSGQSTNNAVIGTQVLNSGSSGKVQVQVSVNGRPSDLVSAQVILTNELNFALVGSEDGTDNDYNDAVVVINWPLG 114
                                    10        20        30        40        50        60        70        80        90       100       110

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Calcium-mediated lectin (32)

Superfamily: Calcium-mediated lectin (32)

Family: Calcium-mediated lectin (25)

Protein domain: automated matches (14)

Pseudomonas aeruginosa [TaxId: 287] (12)

1a	d1w8fa_	A:
1b	d1w8fb_	B:
1c	d1w8fc_	C:
1d	d1w8fd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Jelly Rolls (1293)

Homologous Superfamily: Calcium-mediated lectin (24)

Pseudomonas aeruginosa. Organism_taxid: 287. (9)

1a	1w8fA00	A:1-114
1b	1w8fB00	B:1-114
1c	1w8fC00	C:1-114
1d	1w8fD00	D:1-114

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: PA-IIL] (21)

Family: PA-IIL (21)

Pseudomonas aeruginosa (17)

1a	PA-IIL-1w8fD01	D:6-113
1b	PA-IIL-1w8fD02	D:6-113
1c	PA-IIL-1w8fD03	D:6-113
1d	PA-IIL-1w8fD04	D:6-113

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (Q9HYN5_PSEAE | Q9HYN5)

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:0046872		metal ion binding		Interacting selectively and non-covalently with any metal ion.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Trp A:111 - Pro A:112	[ RasMol ]
		Trp B:111 - Pro B:112	[ RasMol ]
		Trp C:111 - Pro C:112	[ RasMol ]
		Trp D:111 - Pro D:112	[ RasMol ]

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	1w8f
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1gzt	PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) TOGETHER WITH FUCOSE
1our	LECB (PA-LII) IN COMPLEX WITH MANNOSE
1ous	LECB (PA-LII) CALCIUM-FREE
1oux	LECB (PA-LII) SUGAR-FREE
1ovp	LECB (PA-LII) IN COMPLEX WITH FRUCTOSE
1ovs	LECB (PA-LII) IN COMPLEX WITH CORE TRIMANNOSIDE
1oxc	LECB (PA-LII) IN COMPLEX WITH FUCOSE
1uzv	HIGH AFFINITY FUCOSE BINDING OF PSEUDOMONAS AERUGINOSA LECTIN II: 1.0 A CRYSTAL STRUCTURE OF THE COMPLEX
1w38	PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL) COMPLEXED WITH LACTO-N-NEO-FUCOPENTAOSE V ( LNPF V)
1w43	STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LEWISA TRISACCHARIDE
1w8h	STRUCTURE OF PSEUDOMONAS AERUGINOSA LECTIN II (PA-IIL)COMPLEXED WITH LEWISA TRISACCHARIDE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 31)

Sites (31, 31)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (2, 2)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File