1VPV - JenaLib

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Title :   CRYSTAL STRUCTURE OF A DEGV LIPID BINDING PROTEIN (TM1468) FROM THERMOTOGA MARITIMA AT 2.45 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   18 Nov 04 (Deposition) - 07 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.45

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

Keywords :   Dak1/Degv-Like Fold, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Upf0230 Protein Tm1468 (Tm1468) From Thermotoga Maritima At 2. 45 A Resolution
To Be Published
PubMed: search

Molecule 1 - UPF0230 PROTEIN TM1468
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TM1468
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 16)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
2	PLM	2	Ligand/Ion	PALMITIC ACID
3	PO4	2	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	PLM	1	Ligand/Ion	PALMITIC ACID
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
2	PLM	1	Ligand/Ion	PALMITIC ACID
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:55 , TYR A:169 , LYS B:188 , ARG B:190 , HOH B:524	BINDING SITE FOR RESIDUE PO4 B 289
2	AC2	SOFTWARE	LYS A:188 , ARG A:190 , HOH A:506 , HOH A:531 , ARG B:55 , TYR B:169	BINDING SITE FOR RESIDUE PO4 A 289
3	AC3	SOFTWARE	LEU A:28 , THR A:63 , SER A:64 , GLN A:65 , SER A:96 , SER A:122 , GLY A:123 , ALA A:124 , PHE A:162 , ARG A:175 , MSE A:264 , HIS A:271 , PHE A:279 , GLY A:280 , HOH A:525	BINDING SITE FOR RESIDUE PLM A 501
4	AC4	SOFTWARE	LEU B:28 , THR B:63 , SER B:64 , SER B:96 , SER B:122 , GLY B:123 , PHE B:162 , ARG B:175 , VAL B:235 , HIS B:271 , VAL B:272 , PHE B:279 , GLY B:280 , HOH B:554	BINDING SITE FOR RESIDUE PLM B 501

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

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

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1468_THEMA	3-283	2	A:3-283 B:3-283

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1468_THEMA	3-283	1	A:3-283 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DEGV	PS51482	DegV domain profile.	Y1468_THEMA	3-283	1	- B:3-283

(no "Exon" information available for 1VPV)

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:282
 aligned with Y1468_THEMA | Q9X1H9 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       
          Y1468_THEMA     1 MKVKILVDSTADVPFSWMEKYDIDSIPLYVVWEDGRSEPDEREPEEIMNFYKRIREAGSVPKTSQPSVEDFKKRYLKYKEEDYDVVLVLTLSSKLSGTYNSAVLASKEVDIPVYVVDTLLASGAIPLPARVAREMLENGATIEEVLKKLDERMKNKDFKAIFYVSNFDYLVKGGRVSKFQGFVGNLLKIRVCLHIENGELIPYRKVRGDKKAIEALIEKLREDTPEGSKLRVIGVHADNEAGVVELLNTLRKSYEVVDEIISPMGKVITTHVGPGTVGFGIEVLERK 287
               SCOP domains d1vpva_ A: Hypothetical protein TM841                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -1vpvA01 A:2-154  [code=3.40.50.10170, no name defined]                                                                                                   1vpvA02 A:155-287  [co     de=3.30.1180.10, no name defined]                                                                          CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.hhh...hhhhhh.eeee..eee.....eee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhh..-----.......eeeeeeee..eeeeeeeeehhhhhhhhhhhhhh.......eeeeeeee..hhhhhhhhhhhhhh..eeeeeeeee.hhhhhhhhh...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DEGV  PDB: A:3-283 UniProt: 3-283                                                                                                                                                                                                                                                        ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpv A   1 mKVKILVDSTADVPFSWmEKYDIDSIPLYVVWEDGRSEPDEREPEEImNFYKRIREAGSVPKTSQPSVEDFKKRYLKYKEEDYDVVLVLTLSSKLSGTYNSAVLASKEVDIPVYVVDTLLASGAIPLPARVAREmLENGATIEEVLKKLDERmKNKDFKAIFYVSNFDYLVKGGRV-----FVGNLLKIRVCLHIENGELIPYRKVRGDKKAIEALIEKLREDTPEGSKLRVIGVHADNEAGVVELLNTLRKSYEVVDEIISPmGKVITTHVGPGTVGFGIEVLERK 287
                            |       10       |20        30        40       |50        60        70        80        90       100       110       120       130    |  140       150  |    160       170     |   - |     190       200       210       220       230       240       250       260   |   270       280       
                            |               18-MSE                        48-MSE                                                                                135-MSE           153-MSE                176   182                                                                               264-MSE                   
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:278
 aligned with Y1468_THEMA | Q9X1H9 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       
          Y1468_THEMA     1 MKVKILVDSTADVPFSWMEKYDIDSIPLYVVWEDGRSEPDEREPEEIMNFYKRIREAGSVPKTSQPSVEDFKKRYLKYKEEDYDVVLVLTLSSKLSGTYNSAVLASKEVDIPVYVVDTLLASGAIPLPARVAREMLENGATIEEVLKKLDERMKNKDFKAIFYVSNFDYLVKGGRVSKFQGFVGNLLKIRVCLHIENGELIPYRKVRGDKKAIEALIEKLREDTPEGSKLRVIGVHADNEAGVVELLNTLRKSYEVVDEIISPMGKVITTHVGPGTVGFGIEVLERK 287
               SCOP domains d1vpvb_ B: Hypothetical protein TM841                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -1vpvB01 B:2-154  [code=3.40.50.10170, no name defined]                                                                                                   1vpvB02 B:155-287  [co         de=3.30.1180.10, no name defined]                                                                      CATH domains
           Pfam domains (1) -------------------------------------------------------------------------DegV-1vpvB01 B:74-284                                                                                                                                                                                              --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------------DegV-1vpvB02 B:74-284                                                                                                                                                                                              --- Pfam domains (2)
         Sec.struct. author ..eeeeee.hhh...hhhhhh.eeee..eee.....eee...hhhhhhhhhhhhhhh....eee..hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhh..---------...eeeeeeee..eeeeeeeeehhhhhhhhhhhhhhh......eeeeeeee..hhhhhhhhhhhhh...eeeeeeeee.hhhhhhhhh...eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --DEGV  PDB: B:3-283 UniProt: 3-283                                                                                                                                                                                                                                                        ---- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vpv B   1 mKVKILVDSTADVPFSWmEKYDIDSIPLYVVWEDGRSEPDEREPEEImNFYKRIREAGSVPKTSQPSVEDFKKRYLKYKEEDYDVVLVLTLSSKLSGTYNSAVLASKEVDIPVYVVDTLLASGAIPLPARVAREmLENGATIEEVLKKLDERmKNKDFKAIFYVSNFDYLVKGGRV---------LLKIRVCLHIENGELIPYRKVRGDKKAIEALIEKLREDTPEGSKLRVIGVHADNEAGVVELLNTLRKSYEVVDEIISPmGKVITTHVGPGTVGFGIEVLERK 287
                            |       10       |20        30        40       |50        60        70        80        90       100       110       120       130    |  140       150  |    160       170     |   -     | 190       200       210       220       230       240       250       260   |   270       280       
                            1-MSE           18-MSE                        48-MSE                                                                                135-MSE           153-MSE                176       186                                                                           264-MSE

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

Fold: DAK1/DegV-like (26)

Superfamily: DAK1/DegV-like (26)

Family: DegV-like (3)

Protein domain: Hypothetical protein TM841 (2)

Thermotoga maritima [TaxId: 2336] (2)

1a	d1vpva_	A:
1b	d1vpvb_	B:

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: EDD (22)

Family: DegV (6)

Thermotoga maritima (2)

1a	DegV-1vpvB01	B:74-284
1b	DegV-1vpvB02	B:74-284

Asymmetric Unit(hide GO term definitions)

Chain A,B (Y1468_THEMA | Q9X1H9)

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

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vpv)

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Description

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Ligands, Modified Residues, Ions (3, 16)

Sites (4, 4)

SS Bonds (0, 0)

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