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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   FLO5A SHOWING A TRINUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE

Authors :   M. Veelders, L. -O. Essen

Date :   07 Feb 12 (Deposition) - 30 Jan 13 (Release) - 28 Jun 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Sugar Binding Protein, Adhesin, Flocculin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Veelders, L. Essen
Complex Gadolinium-Oxo Clusters Formed Along Concave Protei Surfaces.
Chembiochem V. 13 2187 2012
PubMed-ID: 22936626 | Reference-DOI: 10.1002/CBIC.201200441

Molecule 1 - FLOCCULATION PROTEIN FLO5
	Atcc	:	204508
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Variant	:	ORIGAMI 2
	Expression System Vector	:	PET28A
	Expression System Vector Type	:	PLASMID
	Fragment	:	LECTIN-LIKE DOMAIN, RESIDUES 23-271
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	559292
	Other Details	:	SOAKED WITH GDAC3
	Strain	:	S288C
	Synonym	:	FLOCCULIN-5, FLO5A

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	CL	2	Ligand/Ion	CHLORIDE ION
3	GD	8	Ligand/Ion	GADOLINIUM ATOM

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:160 , ASP A:161 , ASN A:224 , VAL A:226 , TRP A:228 , HOH A:2281 , HOH A:2284 , HOH A:2343	BINDING SITE FOR RESIDUE GD A 1272
02	AC2	SOFTWARE	ASP A:78 , ASP A:245 , HOH A:2153 , HOH A:2155 , HOH A:2156 , HOH A:2164 , HOH A:2167 , HOH A:2360	BINDING SITE FOR RESIDUE GD A 1273
03	AC3	SOFTWARE	ASP A:82 , ASP A:125 , ACT A:1282 , HOH A:2163	BINDING SITE FOR RESIDUE GD A 1274
04	AC4	SOFTWARE	ASP A:125 , ACT A:1282 , HOH A:2242 , HOH A:2246 , HOH A:2247 , HOH A:2249 , HOH A:2398 , HOH A:2399	BINDING SITE FOR RESIDUE GD A 1275
05	AC5	SOFTWARE	GLU A:236 , HOH A:2346 , HOH A:2347 , HOH A:2350	BINDING SITE FOR RESIDUE GD A 1276
06	AC6	SOFTWARE	GLU A:179 , ASP A:255 , HOH A:2302 , HOH A:2304 , HOH A:2306 , HOH A:2371	BINDING SITE FOR RESIDUE GD A 1277
07	AC7	SOFTWARE	SER A:170 , GLU A:174 , HOH A:2040 , HOH A:2288 , HOH A:2292 , HOH A:2400	BINDING SITE FOR RESIDUE GD A 1278
08	AC8	SOFTWARE	GLU A:99 , HOH A:2171 , HOH A:2172 , HOH A:2173 , HOH A:2201 , HOH A:2401	BINDING SITE FOR RESIDUE GD A 1279
09	AC9	SOFTWARE	TYR A:102 , CYS A:107 , GLY A:109 , GLY A:111	BINDING SITE FOR RESIDUE CL A 1280
10	BC1	SOFTWARE	PHE A:94 , PRO A:95 , HOH A:2177 , HOH A:2189	BINDING SITE FOR RESIDUE CL A 1281
11	BC2	SOFTWARE	SER A:80 , ASP A:82 , ASP A:125 , GD A:1274 , GD A:1275 , HOH A:2246 , HOH A:2398	BINDING SITE FOR RESIDUE ACT A 1282

Asymmetric/Biological Unit

No.	Residues
1	A:29	-	A:175
2	A:87	-	A:113
3	A:96	-	A:107
4	A:176	-	A:263

Asymmetric/Biological Unit

No.	Residues
1	Asn A:104	-	Trp A:105
2	Asp A:160	-	Asp A:161

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA14	PS51820	PA14 domain profile.	FLO5_YEAST	74-249	1	A:74-249

(no "Exon" information available for 4AHX)

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:258
 aligned with FLO5_YEAST | P38894 from UniProtKB/Swiss-Prot  Length:1075

    Alignment length:258
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263        
           FLO5_YEAST    14 AFLALINVASGATEACLPAGQRKSGMNINFYQYSLKDSSTYSNAAYMAYGYASKTKLGSVGGQTDISIDYNIPCVSSSGTFPCPQEDSYGNWGCKGMGACSNSQGIAYWSTDLFGFYTTPTNVTLEMTGYFLPPQTGSYTFSFATVDDSAILSVGGSIAFECCAQEQPPITSTNFTINGIKPWDGSLPDNITGTVYMYAGYYYPLKVVYSNAVSWGTLPISVELPDGTTVSDNFEGYVYSFDDDLSQSNCTIPDPSIH 271
               SCOP domains d4ahxa_ A: automated matches                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhh...ee......ee.eeeeeee......hhhhhhhhhhhhhhhh.eeeeeeee....eee..eeee..eeee.hhh.ee...ee...ee.......................eeeeeeeee.....eeeeeee.....eeeeee......................eee...........eeeeeee.....eeeeeeeee....eee.eeee.....eee......eee..........ee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------PA14  PDB: A:74-249 UniProt: 74-249                                                                                                                                             ---------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ahx A  14 GLVPRGSHMSGATEACLPAGQRKSGMNINFYQYSLKDSSTYSNAAYMAYGYASKTKLGSVGGQTDISIDYNIPCVSSSGTFPCPQEDSYGNWGCKGMGACSNSQGIAYWSTDLFGFYTTPTNVTLEMTGYFLPPQTGSYTFSFATVDDSAILSVGGSIAFECCAQEQPPITSTNFTINGIKPWDGSLPDNITGTVYMYAGYYYPLKVVYSNAVSWGTLPISVELPDGTTVSDNFEGYVYSFDDDLSQSNCTIPDPSIH 271
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Anthrax protective antigen N-terminal-like (32)

Superfamily: PA14-like (32)

Family: GLEYA domain (15)

Protein domain: automated matches (8)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 559292] (8)

d4ahxa_

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (FLO5_YEAST | P38894)

molecular function
	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.
biological process
	GO:0031589	cell-substrate adhesion	The attachment of a cell to the underlying substrate via adhesion molecules.
	GO:0036281	coflocculation	The non-sexual aggregation between single-celled organisms of different species.
	GO:0000128	flocculation	The reversible, non-sexual aggregation of single-celled organisms in suspension to form aggregates of many cells known as flocs.
	GO:0000501	flocculation via cell wall protein-carbohydrate interaction	The reversible, non-sexual aggregation of cells mediated by the binding of proteins in the cell wall of one cell to carbohydrates in the cell wall of another cell. An example of this process is found in Saccharomyces cerevisiae, in which it is pH- and calcium-dependent.
cellular component
	GO:0031225	anchored component of membrane	The component of a membrane consisting of the gene products that are tethered to the membrane only by a covalently attached anchor, such as a lipid group that is embedded in the membrane. Gene products with peptide sequences that are embedded in the membrane are excluded from this grouping.
	GO:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0009277	fungal-type cell wall	A rigid yet dynamic structure surrounding the plasma membrane that affords protection from stresses and contributes to cell morphogenesis, consisting of extensively cross-linked glycoproteins and carbohydrates. The glycoproteins may be modified with N- or O-linked carbohydrates, or glycosylphosphatidylinositol (GPI) anchors; the polysaccharides are primarily branched glucans, including beta-linked and alpha-linked glucans, and may also include chitin and other carbohydrate polymers, but not cellulose or pectin. Enzymes involved in cell wall biosynthesis are also found in the cell wall. Note that some forms of fungi develop a capsule outside of the cell wall under certain circumstances; this is considered a separate structure.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Asn A:104 - Trp A:105	[ RasMol ]
		Asp A:160 - Asp A:161	[ RasMol ]

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Access by PDB/NDB ID
	4ahx
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
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Access by UniProt ID/Accession number
	FLO5_YEAST \| P38894
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	FLO5_YEAST \| P38894
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UniProtKB/Swiss-Prot
	FLO5_YEAST \| P38894	:	2xjp 2xjq 2xjr 2xjs 2xjt 2xju 2xjv 4ahw 4ahy 4ahz 4ai0 4ai1 4ai2 4ai3

4ahw	FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE
4ahy	FLO5A COCRYSTALLIZED WITH 3 MM GDAC3
4ahz	FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 60 MIN OF SOAKING
4ai0	FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 9 MIN OF SOAKING
4ai1	FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 19 MIN OF SOAKING
4ai2	FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 41 MIN OF SOAKING
4ai3	FLO5A SHOWING A HEPTANUCLEAR GADOLINIUM CLUSTER ON ITS SURFACE AFTER 60 MIN OF SOAKING

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (11, 11)

SS Bonds (4, 4)

Cis Peptide Bonds (2, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File