3MCY - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF FIMH LECTIN DOMAIN BOUND TO BIPHENYL MANNOSIDE META-METHYL ESTER.

Authors :   B. A. Ford, S. J. Hultgren

Date :   29 Mar 10 (Deposition) - 16 Jun 10 (Release) - 21 Jul 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Lectin, Mannoside, Immunogobulin Fold, Carbohydrate Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Han, J. S. Pinkner, B. Ford, R. Obermann, W. Nolan, S. A. Wildman, D. Hobbs, T. Ellenberger, C. K. Cusumano, S. J. Hultgren, J. W. Janetka
Structure-Based Drug Design And Optimization Of Mannoside Bacterial Fimh Antagonists.
J. Med. Chem. V. 53 4779 2010
PubMed-ID: 20507142 | Reference-DOI: 10.1021/JM100438S

Molecule 1 - FIMH
	Chains	:	A, D, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTRC99A
	Expression System Strain	:	C600
	Expression System Taxid	:	83333
	Expression System Vector Type	:	PLASMID
	Fragment	:	FIMH LECTIN DOMAIN, UNP RESIDUES 22-196
	Gene	:	FIMH
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Strain	:	J96

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	CA	4	Ligand/Ion	CALCIUM ION
2	CL	3	Ligand/Ion	CHLORIDE ION
3	GOL	3	Ligand/Ion	GLYCEROL
4	ZH1	4	Ligand/Ion	METHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	ZH1	1	Ligand/Ion	METHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	-1	Ligand/Ion	GLYCEROL
4	ZH1	1	Ligand/Ion	METHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE

Biological Unit 3 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	ZH1	1	Ligand/Ion	METHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE

Biological Unit 4 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	1	Ligand/Ion	GLYCEROL
4	ZH1	1	Ligand/Ion	METHYL 4'-(ALPHA-D-MANNOPYRANOSYLOXY)BIPHENYL-3-CARBOXYLATE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:1 , ILE A:13 , ASN A:46 , ASP A:47 , TYR A:48 , ASP A:54 , ARG A:98 , GLN A:133 , ASN A:135 , ASP A:140 , PHE A:142 , HOH A:225 , HOH A:239 , ALA B:122 , ASN B:152	BINDING SITE FOR RESIDUE ZH1 A 182
02	AC2	SOFTWARE	ASN A:33 , SER A:72 , GLY A:73 , THR A:74 , TYR A:108 , THR A:110	BINDING SITE FOR RESIDUE GOL A 183
03	AC3	SOFTWARE	HIS A:45 , ASP A:47 , HOH A:209 , HOH A:210 , HOH A:211 , HOH A:237	BINDING SITE FOR RESIDUE CA A 184
04	AC4	SOFTWARE	HIS A:45	BINDING SITE FOR RESIDUE CL A 185
05	AC5	SOFTWARE	PHE D:1 , ILE D:13 , PRO D:26 , ASN D:46 , ASP D:47 , TYR D:48 , ILE D:52 , ASP D:54 , ARG D:98 , GLN D:133 , ASN D:135 , ASP D:140 , ASN D:151 , ASP D:153 , HOH D:201	BINDING SITE FOR RESIDUE ZH1 D 182
06	AC6	SOFTWARE	HIS D:45 , ASP D:47	BINDING SITE FOR RESIDUE CA D 183
07	AC7	SOFTWARE	PHE B:1 , ILE B:13 , ASN B:46 , ASP B:47 , TYR B:48 , ASP B:54 , ARG B:98 , GLN B:133 , ASN B:135 , ASP B:140 , PHE B:142 , HOH B:222 , PRO C:26 , ALA C:122 , ASN C:152 , ASP C:153 , PRO D:26	BINDING SITE FOR RESIDUE ZH1 B 182
08	AC8	SOFTWARE	SER B:17 , ALA B:18 , ASN B:19	BINDING SITE FOR RESIDUE GOL B 183
09	AC9	SOFTWARE	HIS B:45 , ASP B:47 , HOH B:204 , HOH B:214 , HOH B:230 , HOH B:236	BINDING SITE FOR RESIDUE CA B 184
10	BC1	SOFTWARE	HIS B:45	BINDING SITE FOR RESIDUE CL B 185
11	BC2	SOFTWARE	ALA A:122 , ASN A:152 , PRO B:26 , PHE C:1 , ILE C:13 , ASN C:46 , ASP C:47 , TYR C:48 , ASP C:54 , ARG C:98 , GLN C:133 , ASN C:135 , ASP C:140 , HOH C:186	BINDING SITE FOR RESIDUE ZH1 C 182
12	BC3	SOFTWARE	LYS C:4 , ALA C:6	BINDING SITE FOR RESIDUE GOL C 183
13	BC4	SOFTWARE	HIS C:45 , ASP C:47 , HOH C:195 , HOH C:196 , HOH C:209 , HOH C:212	BINDING SITE FOR RESIDUE CA C 184
14	BC5	SOFTWARE	LYS C:4 , HIS C:45	BINDING SITE FOR RESIDUE CL C 185

Asymmetric Unit

No.	Residues
1	A:3	-	A:44
2	B:3	-	B:44
3	C:3	-	C:44
4	D:3	-	D:44

(no "Cis Peptide Bond" information available for 3MCY)

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

(no "PROSITE Motif" information available for 3MCY)

(no "Exon" information available for 3MCY)

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:158
 aligned with Q9S497_ECOLX | Q9S497 from UniProtKB/TrEMBL  Length:300

    Alignment length:158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
         Q9S497_ECOLX    22 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 179
               SCOP domains d3mcya_ A: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee......eeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcy A   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:158
 aligned with Q9S497_ECOLX | Q9S497 from UniProtKB/TrEMBL  Length:300

    Alignment length:158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
         Q9S497_ECOLX    22 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 179
               SCOP domains d3mcyb_ B: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee......eeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcy B   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:158
 aligned with Q9S497_ECOLX | Q9S497 from UniProtKB/TrEMBL  Length:300

    Alignment length:158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
         Q9S497_ECOLX    22 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 179
               SCOP domains d3mcyc_ C: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeeeehhhhhhheeeeeee...eee.........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee......eeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcy C   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:158
 aligned with Q9S497_ECOLX | Q9S497 from UniProtKB/TrEMBL  Length:300

    Alignment length:158
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171        
         Q9S497_ECOLX    22 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 179
               SCOP domains d3mcyd_ D: Mannose-specific adhesin FimH                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------------------------------------------------------------------------------------------------------------------Fimbrial-3mcy Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------------------------------------------------------------------------------Fimbrial-3mcy Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------------------------------------------------------------------------------------Fimbrial-3mcy Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------------------------------------------------------------------------------------Fimbrial-3mcy Pfam domains (4)
           Pfam domains (5) --FimH_man-bind-3mcyD05 D:3-147                                                                                                                    ----------- Pfam domains (5)
           Pfam domains (6) --FimH_man-bind-3mcyD06 D:3-147                                                                                                                    ----------- Pfam domains (6)
           Pfam domains (7) --FimH_man-bind-3mcyD07 D:3-147                                                                                                                    ----------- Pfam domains (7)
           Pfam domains (8) --FimH_man-bind-3mcyD08 D:3-147                                                                                                                    ----------- Pfam domains (8)
         Sec.struct. author .eeee....ee....eeeeeee...........eeee....eeee........eeeeeeeee.hhhhhhheeeeeee..eeeee........eee.....ee..eeeeeee.....eeee....eeeeeeeeeee.....eeeeeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcy D   1 FACKTANGTAIPIGGGSANVYVNLAPVVNVGQNLVVDLSTQIFCHNDYPETITDYVTLQRGSAYGGVLSNFSGTVKYSGSSYPFPTTSETPRVVYNSRTDKPWPVALYLTPVSSAGGVAIKAGSLIAVLILRQTNNYNSDDFQFVWNIYANNDVVVPT 158
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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: Common fold of diphtheria toxin/transcription factors/cytochrome f (364)

Superfamily: Bacterial adhesins (93)

Family: Pilus subunits (59)

Protein domain: Mannose-specific adhesin FimH (22)

Escherichia coli [TaxId: 562] (22)

1a	d3mcya_	A:
1b	d3mcyb_	B:
1c	d3mcyc_	C:
1d	d3mcyd_	D:

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

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Adhesin (36)

Family: Fimbrial (23)

Escherichia coli (15)

1a	Fimbrial-3mcyD01	D:146-158
1b	Fimbrial-3mcyD02	D:146-158
1c	Fimbrial-3mcyD03	D:146-158
1d	Fimbrial-3mcyD04	D:146-158

Clan: no clan defined [family: FimH_man-bind] (6)

Family: FimH_man-bind (6)

Escherichia coli (2)

2a	FimH_man-bind-3mcyD05	D:3-147
2b	FimH_man-bind-3mcyD06	D:3-147
2c	FimH_man-bind-3mcyD07	D:3-147
2d	FimH_man-bind-3mcyD08	D:3-147

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q9S497_ECOLX | Q9S497)

biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
cellular component
	GO:0009289	pilus	A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (4, 14)

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SS Bonds (4, 4)

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