2G7Z - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CONSERVED DEGV-LIKE PROTEIN OF UNKNOWN FUNCTION FROM STREPTOCOCCUS PYOGENES M1 GAS BINDS LONG-CHAIN FATTY ACIDS

Authors :   B. Nocek, L. Volkart, S. Clancy, A. Joachimiak, Midwest Center For S Genomics (Mcsg)

Date :   01 Mar 06 (Deposition) - 04 Apr 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.05

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

Keywords :   Long-Fatty Acid Binding Protein, Lipid Binding Protein, Psi, Mcsg, Hypothetical Protein, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. Nocek, L. Volkart, S. Clancy, A. Joachimiak
Conserved Hypothetical Protein From Streptococcus Pyogenes M1 Gas Discloses Long-Fatty Acid (Heptadecanoic Acid) Binding Function
To Be Published
PubMed: search

Molecule 1 - CONSERVED HYPOTHETICAL PROTEIN SPY1493
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	STREPTOCOCCUS PYOGENES
	Organism Taxid	:	160490
	Strain	:	M1 GAS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 38)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	HXA	2	Ligand/Ion	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
4	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
5	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6	ZN	16	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	HXA	1	Ligand/Ion	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
4	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (4, 11)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	2	Ligand/Ion	GLYCEROL
3	HXA	1	Ligand/Ion	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
4	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (4, 10)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	HXA	1	Ligand/Ion	DOCOSA-4,7,10,13,16,19-HEXAENOIC ACID
4	MSE	7	Mod. Amino Acid	SELENOMETHIONINE
5	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
6	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLU A:15 , CL A:7001 , HOH A:9143 , ARG B:102 , GLU B:106	BINDING SITE FOR RESIDUE ZN A 6001
02	AC2	SOFTWARE	HIS A:48 , HIS A:222 , HOH A:9150 , HOH A:9359	BINDING SITE FOR RESIDUE ZN A 6002
03	AC3	SOFTWARE	ASP A:84 , HOH A:9306 , HIS B:252 , GOL B:2649 , HOH B:8346	BINDING SITE FOR RESIDUE ZN A 6003
04	AC4	SOFTWARE	GLU A:17 , HOH A:9307 , HOH A:9316 , HOH A:9360	BINDING SITE FOR RESIDUE ZN A 6004
05	AC5	SOFTWARE	GLU A:106 , GLU B:15 , HOH B:8139 , HOH B:8326	BINDING SITE FOR RESIDUE ZN A 6005
06	AC6	SOFTWARE	GLU A:227 , HOH A:9137 , HOH A:9374 , GLU B:109	BINDING SITE FOR RESIDUE ZN A 6006
07	AC7	SOFTWARE	GLU A:143 , HOH A:9309	BINDING SITE FOR RESIDUE ZN A 6007
08	AC8	SOFTWARE	GLU A:109 , HOH A:9139 , GLU B:227 , HOH B:8342	BINDING SITE FOR RESIDUE ZN A 6008
09	AC9	SOFTWARE	ASN A:251 , HIS A:252 , ASP B:84 , HOH B:8137 , HOH B:8312	BINDING SITE FOR RESIDUE ZN B 6009
10	BC1	SOFTWARE	GLU B:17 , HOH B:8318	BINDING SITE FOR RESIDUE ZN B 6010
11	BC2	SOFTWARE	ASP A:23 , HOH A:9198 , HOH A:9365 , HOH A:9366 , HOH A:9377	BINDING SITE FOR RESIDUE ZN A 6011
12	BC3	SOFTWARE	GLU A:235 , GLU A:269 , HOH A:9149 , HOH A:9367	BINDING SITE FOR RESIDUE ZN A 6012
13	BC4	SOFTWARE	ASP A:195 , GLU A:196 , ASP B:195 , GLU B:196	BINDING SITE FOR RESIDUE ZN A 6013
14	BC5	SOFTWARE	HIS B:48 , HIS B:222 , HOH B:8319 , HOH B:8321	BINDING SITE FOR RESIDUE ZN B 6014
15	BC6	SOFTWARE	ASP B:23 , HOH B:8349 , HOH B:8350	BINDING SITE FOR RESIDUE ZN B 6015
16	BC7	SOFTWARE	GLU B:235 , GLU B:269 , HOH B:8341	BINDING SITE FOR RESIDUE ZN B 6016
17	BC8	SOFTWARE	GLU A:15 , LYS A:125 , ZN A:6001 , GLU B:106	BINDING SITE FOR RESIDUE CL A 7001
18	BC9	SOFTWARE	THR A:62 , SER A:63 , LEU A:94 , SER A:95 , ARG A:172 , ILE A:262 , ILE A:263 , HIS A:266 , PHE A:272 , ALA A:273 , TRS A:5081	BINDING SITE FOR RESIDUE HXA A 9136
19	CC1	SOFTWARE	LEU B:29 , THR B:62 , SER B:63 , GLN B:64 , LEU B:94 , SER B:95 , ILE B:159 , ARG B:172 , ILE B:262 , ILE B:263 , HIS B:266 , ALA B:273 , TRS B:5080	BINDING SITE FOR RESIDUE HXA B 8136
20	CC2	SOFTWARE	SER B:63 , GLN B:64 , SER B:95 , GLY B:96 , ARG B:172 , HXA B:8136	BINDING SITE FOR RESIDUE TRS B 5080
21	CC3	SOFTWARE	SER A:63 , GLN A:64 , SER A:95 , GLY A:96 , ARG A:172 , HXA A:9136 , HOH A:9196	BINDING SITE FOR RESIDUE TRS A 5081
22	CC4	SOFTWARE	PRO A:60 , LYS A:61 , THR A:62 , GLY A:170 , HIS A:266 , HOH A:9196 , HOH A:9380	BINDING SITE FOR RESIDUE GOL A 2647
23	CC5	SOFTWARE	PRO B:60 , LYS B:61 , THR B:62 , GLY B:170 , HIS B:266 , HOH B:8201	BINDING SITE FOR RESIDUE GOL B 2648
24	CC6	SOFTWARE	ZN A:6003 , HOH A:9306 , ASN B:251 , HIS B:252 , HOH B:8283 , HOH B:8346	BINDING SITE FOR RESIDUE GOL B 2649

(no "SS Bond" information available for 2G7Z)

(no "Cis Peptide Bond" information available for 2G7Z)

(no "SAP(SNP)/Variant" information available for 2G7Z)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1493_STRP1	4-278	2	A:4-278 B:4-278

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1493_STRP1	4-278	1	A:4-278 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1493_STRP1	4-278	1	- B:4-278

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1493_STRP1	4-278	2	A:4-278 B:4-278

(no "Exon" information available for 2G7Z)

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
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Chain A from PDB  Type:PROTEIN  Length:275
 aligned with Y1493_STRP1 | P67372 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:280
                             1                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
          Y1493_STRP1     - -MGTIKIVTDSSITIEPELIKALDITVVPLSVMIDSKLYSDNDLKEEGHFLSLMKASKSLPKTSQPPVGLFAETYENLVKKGVTDIVAIHLSPALSGTIEASRQGAEIAEAPVTVLDSGFTDQAMKFQVVEAAKMAKAGASLNEILAAVQAIKSKTELYIGVSTLENLVKGGRIGRVTGVLSSLLNVKVVMALKNDELKTLVKGRGNKTFTKWLDSYLAKNSHRPIAEIAISYAGEASLALTLKERIAAYYNHSISVLETGSIIQTHTGEGAFAVMVRYE 279
               SCOP domains d2g7za_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------2g7zA02 A:155-279  [code     =3.30.1180.10, no name defined]                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhh.eee..eeee..eeee.hhh...hhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhh.ee.-----...eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhh.......eeee.hhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DEGV  PDB: A:4-278 UniProt: 4-278                                                                                                                                                                                                                                                  - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g7z A   0 AmGTIKIVTDSSITIEPELIKALDITVVPLSVmIDSKLYSDNDLKEEGHFLSLmKASKSLPKTSQPPVGLFAETYENLVKKGVTDIVAIHLSPALSGTIEASRQGAEIAEAPVTVLDSGFTDQAmKFQVVEAAKmAKAGASLNEILAAVQAIKSKTELYIGVSTLENLVKGGRIGRVTG-----LNVKVVmALKNDELKTLVKGRGNKTFTKWLDSYLAKNSHRPIAEIAISYAGEASLALTLKERIAAYYNHSISVLETGSIIQTHTGEGAFAVmVRYE 279
                             |       9        19        29  |     39        49   |    59        69        79        89        99       109       119    |  129    |  139       149       159       169        |-    |  189|      199       209       219       229       239       249       259       269     | 279
                             |                             32-MSE               53-MSE                                                                124-MSE   134-MSE                                     178   184     |                                                                                  275-MSE
                             1-MSE                                                                                                                                                                                      190-MSE

Chain B from PDB  Type:PROTEIN  Length:275
 aligned with Y1493_STRP1 | P67372 from UniProtKB/Swiss-Prot  Length:279

    Alignment length:280
                             1                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279
          Y1493_STRP1     - -MGTIKIVTDSSITIEPELIKALDITVVPLSVMIDSKLYSDNDLKEEGHFLSLMKASKSLPKTSQPPVGLFAETYENLVKKGVTDIVAIHLSPALSGTIEASRQGAEIAEAPVTVLDSGFTDQAMKFQVVEAAKMAKAGASLNEILAAVQAIKSKTELYIGVSTLENLVKGGRIGRVTGVLSSLLNVKVVMALKNDELKTLVKGRGNKTFTKWLDSYLAKNSHRPIAEIAISYAGEASLALTLKERIAAYYNHSISVLETGSIIQTHTGEGAFAVMVRYE 279
               SCOP domains d2g7zb_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains -----------------------------------------------------------------------------------------------------------------------------------------------------------2g7zB02 B:155-279  [code=     3.30.1180.10, no name defined]                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....hhhhhhhhh.eee..eeee..eeee.hhh...hhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhheeeeeee..hhhhhhhhhhh.ee..-----..eeeeeee..eeeeeeee..hhhhhhhhhhhhhhhh...eeeeeeeee..hhhhhhhhhhhh.......eeee.hhhhhhhhh..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----DEGV  PDB: B:4-278 UniProt: 4-278                                                                                                                                                                                                                                                  - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g7z B   0 AmGTIKIVTDSSITIEPELIKALDITVVPLSVmIDSKLYSDNDLKEEGHFLSLmKASKSLPKTSQPPVGLFAETYENLVKKGVTDIVAIHLSPALSGTIEASRQGAEIAEAPVTVLDSGFTDQAmKFQVVEAAKmAKAGASLNEILAAVQAIKSKTELYIGVSTLENLVKGGRIGRVTGV-----NVKVVmALKNDELKTLVKGRGNKTFTKWLDSYLAKNSHRPIAEIAISYAGEASLALTLKERIAAYYNHSISVLETGSIIQTHTGEGAFAVmVRYE 279
                             |       9        19        29  |     39        49   |    59        69        79        89        99       109       119    |  129    |  139       149       159       169       179     | 189|      199       209       219       229       239       249       259       269     | 279
                             1-MSE                         32-MSE               53-MSE                                                                124-MSE   134-MSE                                      179   185    |                                                                                  275-MSE
                                                                                                                                                                                                                        190-MSE

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Asymmetric Unit

Classes(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: DAK1/DegV-like (26)

Superfamily: DAK1/DegV-like (26)

Family: automated matches (11)

Protein domain: automated matches (11)

Streptococcus pyogenes [TaxId: 160490] (1)

1a	d2g7za_	A:
1b	d2g7zb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Hypothetical Protein Tm841; Chain: A;domain 3 (10)

Homologous Superfamily: [code=3.30.1180.10, no name defined] (6)

Streptococcus pyogenes serotype m1. Organism_taxid: 301447. Strain: gas. (1)

1a	2g7zA02	A:155-279
1b	2g7zB02	B:155-279

(no "Pfam Domain" information available for 2G7Z)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y1493_STRP1 | P67372)

molecular function
	GO:0008289		lipid binding		Interacting selectively and non-covalently with a lipid.

Asymmetric Unit
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1mgp	HYPOTHETICAL PROTEIN TM841 FROM THERMOTOGA MARITIMA REVEALS FATTY ACID BINDING FUNCTION RELATED ID: APC80011 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 38)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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PROSITE Motifs (1, 2)

Exons (0, 0)

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