1YN8 - JenaLib

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Biological Unit 5 (Jmol Viewer)

Biological Unit 6 (Jmol Viewer)

Title :   SH3 DOMAIN OF YEAST NBP2

Authors :   P. Kursula, I. Kursula, Y. H. Song, M. Wilmanns

Date :   24 Jan 05 (Deposition) - 30 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)
Biol. Unit 6: F  (1x)

Keywords :   Sh3 Domain, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Kursula, I. Kursula, P. Zou, F. Lehmann, Y. H. Song, M. Wilmanns
Structural Analysis Of The Yeast Sh3 Domain Proteome
To Be Published
PubMed: search

Molecule 1 - NAP1-BINDING PROTEIN 2
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PDEST-17
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	SH3 DOMAIN
	Organism Common	:	BAKER'S YEAST
	Organism Scientific	:	SACCHAROMYCES CEREVISIAE
	Organism Taxid	:	4932
	Synonym	:	NBP2

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E
Biological Unit 6 (1x)	:						F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 10)

No.	Name	Count	Type	Full Name
1	CA	10	Ligand/Ion	CALCIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Biological Unit 6 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU B:53 , HOH B:1018 , HOH B:1052 , HOH B:1065 , HOH E:1051 , HOH E:1066 , HOH E:1096	BINDING SITE FOR RESIDUE CA B 1003
02	AC2	SOFTWARE	GLU B:22 , HOH B:1026 , HOH B:1041 , HOH B:1077 , GLU E:13 , CA E:1005 , HOH E:1031 , HOH E:1052 , HOH E:1074	BINDING SITE FOR RESIDUE CA B 1004
03	AC3	SOFTWARE	GLU B:13 , HOH B:1027 , HOH B:1050 , HOH B:1087	BINDING SITE FOR RESIDUE CA B 1007
04	AC4	SOFTWARE	GLU B:13 , HOH B:1087 , HOH E:1094	BINDING SITE FOR RESIDUE CA B 1008
05	AC5	SOFTWARE	TYR B:57 , HOH B:1083 , HOH B:1084 , GLU C:53 , HOH C:1068 , HOH C:1069	BINDING SITE FOR RESIDUE CA C 1001
06	AC6	SOFTWARE	GLU D:13 , CA D:1009 , HOH D:1051 , HOH D:1066 , GLU F:22	BINDING SITE FOR RESIDUE CA D 1006
07	AC7	SOFTWARE	GLU D:13 , CA D:1006 , HOH D:1066 , HOH D:1081 , GLU F:22 , HOH F:109	BINDING SITE FOR RESIDUE CA D 1009
08	AC8	SOFTWARE	GLU D:22 , GLU F:13	BINDING SITE FOR RESIDUE CA D 1010
09	AC9	SOFTWARE	ASP E:24 , HOH E:1086 , HOH E:1087 , HOH E:1088 , HOH E:1089 , HOH E:1090 , HOH E:1091 , HOH E:1092	BINDING SITE FOR RESIDUE CA E 1002
10	BC1	SOFTWARE	GLU B:22 , CA B:1004 , HOH B:1047 , GLU E:13 , HOH E:1052 , HOH E:1062 , HOH E:1065	BINDING SITE FOR RESIDUE CA E 1005

(no "SS Bond" information available for 1YN8)

(no "Cis Peptide Bond" information available for 1YN8)

(no "SAP(SNP)/Variant" information available for 1YN8)

(no "PROSITE Motif" information available for 1YN8)

Asymmetric Unit (1, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	YDR162C	1	YDR162C.1	IV:781098-780388	711	NBP2_YEAST	1-236	236	6	A:1-59 B:1-59 C:1-59 D:1-59 E:1-59 F:1-59	59 59 59 59 59 59

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:59
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:59
                                   121       131       141       151       161         
           NBP2_YEAST   112 NQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ 170
               SCOP domains d1yn8a_ A: automated matches                                SCOP domains
               CATH domains 1yn8A00 A:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeeee..eeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-59 UniProt: 1-236 [INCOMPLETE]           Transcript 1
                 1yn8 A   1 GQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ  59
                                    10        20        30        40        50

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:59
                                   121       131       141       151       161         
           NBP2_YEAST   112 NQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ 170
               SCOP domains d1yn8b_ B: automated matches                                SCOP domains
               CATH domains 1yn8B00 B:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeeee..eeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:1-59 UniProt: 1-236 [INCOMPLETE]           Transcript 1
                 1yn8 B   1 GQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ  59
                                    10        20        30        40        50

Chain C from PDB  Type:PROTEIN  Length:59
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:59
                                   121       131       141       151       161         
           NBP2_YEAST   112 NQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ 170
               SCOP domains d1yn8c_ C: automated matches                                SCOP domains
               CATH domains 1yn8C00 C:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeee...eeeeee.....eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:1-59 UniProt: 1-236 [INCOMPLETE]           Transcript 1
                 1yn8 C   1 GQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ  59
                                    10        20        30        40        50

Chain D from PDB  Type:PROTEIN  Length:59
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:59
                                   121       131       141       151       161         
           NBP2_YEAST   112 NQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ 170
               SCOP domains d1yn8d_ D: automated matches                                SCOP domains
               CATH domains 1yn8D00 D:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeeee..eeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:1-59 UniProt: 1-236 [INCOMPLETE]           Transcript 1
                 1yn8 D   1 GQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ  59
                                    10        20        30        40        50

Chain E from PDB  Type:PROTEIN  Length:59
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:59
                                   121       131       141       151       161         
           NBP2_YEAST   112 NQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ 170
               SCOP domains d1yn8e_ E: automated matches                                SCOP domains
               CATH domains 1yn8E00 E:1-59 SH3 Domains                                  CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..................eeeeeeeee..eeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: E:1-59 UniProt: 1-236 [INCOMPLETE]           Transcript 1
                 1yn8 E   1 GQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ  59
                                    10        20        30        40        50

Chain F from PDB  Type:PROTEIN  Length:59
 aligned with NBP2_YEAST | Q12163 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:59
                                   121       131       141       151       161         
           NBP2_YEAST   112 NQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ 170
               SCOP domains d1yn8f_ F: automated matches                                SCOP domains
               CATH domains 1yn8F00 F:1-59 SH3 Domains                                  CATH domains
           Pfam domains (1) ----SH3_1-1yn8F01 F:5-52                            ------- Pfam domains (1)
           Pfam domains (2) ----SH3_1-1yn8F02 F:5-52                            ------- Pfam domains (2)
           Pfam domains (3) ----SH3_1-1yn8F03 F:5-52                            ------- Pfam domains (3)
           Pfam domains (4) ----SH3_1-1yn8F04 F:5-52                            ------- Pfam domains (4)
           Pfam domains (5) ----SH3_1-1yn8F05 F:5-52                            ------- Pfam domains (5)
           Pfam domains (6) ----SH3_1-1yn8F06 F:5-52                            ------- Pfam domains (6)
         Sec.struct. author .eeeee..................eeeeeee....eeeee......eeeee...eee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: F:1-59 UniProt: 1-236 [INCOMPLETE]           Transcript 1
                 1yn8 F   1 GQRAVALYDFEPENDNELRLAEGDIVFISYKHGQGWLVAENESGSKTGLVPEEFVSYIQ  59
                                    10        20        30        40        50

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: SH3-like barrel (1035)

Superfamily: SH3-domain (369)

Family: automated matches (114)

Protein domain: automated matches (114)

Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932] (12)

1a	d1yn8a_	A:
1b	d1yn8b_	B:
1c	d1yn8c_	C:
1d	d1yn8d_	D:
1e	d1yn8e_	E:
1f	d1yn8f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Roll (1513)

Topology: SH3 type barrels. (648)

Homologous Superfamily: SH3 Domains (267)

Baker's yeast (Saccharomyces cerevisiae) (21)

1a	1yn8A00	A:1-59
1b	1yn8B00	B:1-59
1c	1yn8C00	C:1-59
1d	1yn8D00	D:1-59
1e	1yn8E00	E:1-59
1f	1yn8F00	F:1-59

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: SH3 (175)

Family: SH3_1 (141)

Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast) (24)

1a	SH3_1-1yn8F01	F:5-52
1b	SH3_1-1yn8F02	F:5-52
1c	SH3_1-1yn8F03	F:5-52
1d	SH3_1-1yn8F04	F:5-52
1e	SH3_1-1yn8F05	F:5-52
1f	SH3_1-1yn8F06	F:5-52

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (NBP2_YEAST | Q12163)

molecular function
	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).
	GO:0030674	protein binding, bridging	The binding activity of a molecule that brings together two or more protein molecules, or a protein and another macromolecule or complex, through a selective, non-covalent, often stoichiometric interaction, permitting those molecules to function in a coordinated way.
biological process
	GO:0006972	hyperosmotic response	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
	GO:0000200	inactivation of MAPK activity involved in cell wall organization or biogenesis	Any process that terminates the activity of the active enzyme MAP kinase in the context of cell wall organization or biogenesis.
	GO:0000173	inactivation of MAPK activity involved in osmosensory signaling pathway	Any process that terminates the activity of the active enzyme MAP kinase during osmolarity sensing.
	GO:0006469	negative regulation of protein kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of protein kinase activity.
	GO:0009408	response to heat	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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	Cis Peptide Bonds
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