3TP4 - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ENGINEERED PROTEIN AT THE RESOLUTION 1.98A, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR128

Authors :   A. Kuzin, M. Su, J. Seetharaman, S. Rajagopalan, J. K. Everett, R. Nair, T. B. Acton, B. Rost, D. Baker, G. T. Montelione, J. F. Hunt, L. Tong, Nor Structural Genomics Consortium (Nesg)

Date :   07 Sep 11 (Deposition) - 05 Oct 11 (Release) - 14 May 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.98

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

Keywords :   Structural Genomics, Psi-Biology, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Or128, Osh97, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Rajagopalan, C. Wang, K. Yu, A. P. Kuzin, F. Richter, S. Lew, A. E. Miklos, M. L. Matthews, J. Seetharaman, M. Su, J. F. Hunt, B. F. Cravatt, D. Baker
Design Of Activated Serine-Containing Catalytic Triads With Atomic-Level Accuracy.
Nat. Chem. Biol. V. 10 386 2014
PubMed-ID: 24705591 | Reference-DOI: 10.1038/NCHEMBIO.1498

Molecule 1 - COMPUTATIONAL DESIGN OF ENZYME
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET29B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	SYNTHETIC CONSTRUCT
	Organism Taxid	:	32630

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 8)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	MG	1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	-1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACY	1	Ligand/Ion	ACETIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Biological Unit 3 (3, 7)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
4	PEG	1	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA B:347 , ASP B:349 , THR B:352 , HOH B:810	BINDING SITE FOR RESIDUE MG B 476
2	AC2	SOFTWARE	SER A:179 , TRP A:180 , PHE A:181 , HOH B:788	BINDING SITE FOR RESIDUE ACY A 476
3	AC3	SOFTWARE	GLY B:236 , ASP B:237 , ALA B:238 , HOH B:560 , HOH B:740	BINDING SITE FOR RESIDUE ACY B 477
4	AC4	SOFTWARE	PHE B:117 , VAL B:118 , ASP B:129 , THR B:130 , TRP B:183 , ALA B:185 , HOH B:811	BINDING SITE FOR RESIDUE PEG B 478

(no "SS Bond" information available for 3TP4)

Asymmetric Unit

No.	Residues
1	Arg A:79	-	Pro A:80
2	Ala A:177	-	Gly A:178
3	Ser A:379	-	Pro A:380
4	Ala A:389	-	Pro A:390
5	Arg B:79	-	Pro B:80
6	Ser B:122	-	Phe B:123
7	Ala B:177	-	Gly B:178
8	Ser B:379	-	Pro B:380

(no "SAP(SNP)/Variant" information available for 3TP4)

(no "PROSITE Motif" information available for 3TP4)

(no "Exon" information available for 3TP4)

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:454
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......hhhhhhhhhhhhhhh...eeeeee................hhhhhhhh....eeeee.hhh...........hhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh........hhhhhh....hhhhhhhhhhhhhhhhhhh.........eeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhh.......ee..eeee...hhhhhhhhhhhhhhhhhhhhhhh.ee...eeee............hhhhhhhhhhhh........eeee.................hhhhhhhhhhh..eehhhhh.......eee.....eeeeee.....ee....eeeeeeee...eeeeeeeeee..eeeeeee.ee.....eeeee....eeeeeeee..eeeeeeee.ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tp4 A   3 DETIAIVDADATAETRSLLSYLDGVRGEGILFGHHGTTSSGLTTGPTDGTTSDVKNVTGDFPAVFGWSTSIIEGNQRPGLAENTRDENIALFADYIRKADAIGGVNTVGAGVENFVTGGSFYDDTLRAVLPGGSHHAELVAYLDDIAELADASRRDDGTLIPIVFRPWHENAGSWFWWGAAYGSPGEYQELYRFTVEYLRDVKGVSNFLYAWGPGGGFGGNRDVYLRTYPGDAFVDVLGLDTYDSTGSDAFLAGLVADLRmIAEIADEKGKVSAFTRFGVSGGVGTNGSSPAQWFTKVLAAIKADPVASRNAYmETGENADAGQHFVPVPGDALLEDFQAYAADPFTLFASEVTGAFDRTVAAAPAQPVVHIASPADGARVASAPTTVRVRVGGTDVQSVTVEVAQGGTVVDTLDLAYDGALWWTAPWSPTYTVTATATTAAGTLDVTNEVAAA 467
                                    12        22        32        42        52        62        72        82        92       102       112       122  ||   135       145       155       165       175       185       195       205       215       225       235       245       255       265|      275       285       295       305       315   |   325       335       345       355       365       375       385       395       405       415       425       435|      453       463    
                                                                                                                                                    125|                                                                                                                                      266-MSE                                              319-MSE                                                                                                             435|                       
                                                                                                                                                     129                                                                                                                                                                                                                                                                                                                444

Chain B from PDB  Type:PROTEIN  Length:457
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......hhhhhhhhhhhhhh....eeeeee................hhhhhhhh....eeeee.hhhhh.........hhhhhhhhhhhhhhhhhhhh.eeeeeee.hhhh.....hhhhhhh....hhhhhhhhhhhhhhhhhhh.........eeeeeee........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhh.......ee..eeee...hhhhhhhhhhhhhhhhhhhhhhh.ee...eeee............hhhhhhhhhhhhh.......eeee.................hhhhhhhhhhh..eehhhhh.......eee.....eeeeee.....ee....eeeeeeee...eeeeeeeee....eeeeee.ee.....eeeee......eeeeeeeeee..eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tp4 B   3 DETIAIVDADATAETRSLLSYLDGVRGEGILFGHHGTTSSGLTTGPTDGTTSDVKNVTGDFPAVFGWSTSIIEGNQRPGLAENTRDENIALFADYIRKADAIGGVNTVGAGVENFVGSFYGDTLRAVLPGGSHHAELVAYLDDIAELADASRRDDGTLIPIVFRPWHENAGSWFWWGAAYGSPGEYQELYRFTVEYLRDVKGVSNFLYAWGPGGGFGGNRDVYLRTYPGDAFVDVLGLDTYDSTGSDAFLAGLVADLRmIAEIADEKGKVSAFTRFGVSGGVGTNGSSPAQWFTKVLAAIKADPVASRNAYmETGENADAGQHFVPVPGDALLEDFQAYAADPFTLFASEVTGAFDRTVAAAPAQPVVHIASPADGARVASAPTTVRVRVGGTDVQSVTVEVAQGGTVVDTLDLAYDGALWWTAPWSPTSNSTYTVTATATTAAGTLDVTNEVAAAL 468
                                    12        22        32        42        52        62        72        82        92       102       112     ||124|      137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317 |     327       337       347       357       367       377       387       397       407       417       427       437|      451       461       
                                                                                                                                             118|  ||                                                                                                                                       266-MSE                                              319-MSE                                                                                                               437|                          
                                                                                                                                              121  ||                                                                                                                                                                                                                                                                                                                   442                          
                                                                                                                                                 124|                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                  128

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 '\|'

(no "SCOP Domain" information available for 3TP4)

(no "CATH Domain" information available for 3TP4)

(no "Pfam Domain" information available for 3TP4)

Asymmetric Unit(hide GO term definitions)

(no "Gene Ontology" information available for 3TP4)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACY	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:177 - Gly A:178	[ RasMol ]
		Ala A:389 - Pro A:390	[ RasMol ]
		Ala B:177 - Gly B:178	[ RasMol ]
		Arg A:79 - Pro A:80	[ RasMol ]
		Arg B:79 - Pro B:80	[ RasMol ]
		Ser A:379 - Pro A:380	[ RasMol ]
		Ser B:122 - Phe B:123	[ RasMol ]
		Ser B:379 - Pro B:380	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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2bvy	97% HOMOLOGY RELATED ID: OR128 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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