2D62 - JenaLib

Title :   CRYSTAL STRUCTURE OF MULTIPLE SUGAR BINDING TRANSPORT ATP-BINDING PROTEIN

Authors :   N. K. Lokanath, E. Mizohata, E. Yamaguchi-Sihta, L. Chen, Z. J. Liu, B. C. Wang, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   08 Nov 05 (Deposition) - 08 May 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Atp-Binding, Structural Geomics, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Lokanath, E. Mizohata, E. Yamaguchi-Sihta, L. Chen, Z. J. Liu, B. C. Wang, N. Kunishima
Crystal Structure Of Multiple Sugar Binding Transport Atp-Binding Protein
To Be Published
PubMed: search
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 22)

Sites (8, 8)

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:33 , ASP A:211 , HOH A:1544	BINDING SITE FOR RESIDUE SO4 A 1002
2	AC2	SOFTWARE	PRO A:40 , SER A:41 , HIS A:201 , HOH A:1546	BINDING SITE FOR RESIDUE SO4 A 1003
3	AC3	SOFTWARE	PRO A:97 , HIS A:98 , LYS A:139 , ARG A:141 , HIS A:304	BINDING SITE FOR RESIDUE SO4 A 1004
4	AC4	SOFTWARE	LYS A:110 , LYS A:361 , LYS A:362 , HOH A:1369 , HOH A:1557	BINDING SITE FOR RESIDUE SO4 A 1005
5	AC5	SOFTWARE	GLU A:168 , SER A:171 , ASN A:172 , ARG A:178 , HIS A:201 , HOH A:1460 , HOH A:1461 , HOH A:1567	BINDING SITE FOR RESIDUE SO4 A 1007
6	AC6	SOFTWARE	ASP A:299 , SER A:301 , PHE A:302 , SER A:346 , LYS A:347	BINDING SITE FOR RESIDUE SO4 A 1008
7	AC7	SOFTWARE	ILE A:2 , GLY A:3 , ALA A:5 , GLU A:28 , LYS A:30	BINDING SITE FOR RESIDUE SO4 A 1009
8	AC8	SOFTWARE	PRO A:40 , GLY A:42 , CYS A:43 , GLY A:44 , LYS A:45 , THR A:46 , THR A:47 , HOH A:1357 , HOH A:1373 , HOH A:1548	BINDING SITE FOR RESIDUE POP A 1293

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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:375
 aligned with O57933_PYRHO | O57933 from UniProtKB/TrEMBL  Length:375

    Alignment length:375
                                    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       290       300       310       320       330       340       350       360       370     
         O57933_PYRHO     1 MIGMAEVKLINIWKRFGDVTAVKDLSLEIKDGEFLVLLGPSGCGKTTTLRMIAGLEEPTRGQIYIEDNLVADPEKGVFVPPKERDVAMVFQSYALYPHMTVYDNIAFPLKLRKVPKQEIDKRVREVAEMLGLTELLNRKPRELSGGQRQRVALGRAIIRRPKVFLMDEPLSNLDAKLRVKMRAELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNKGELQQVGTPDEVYYKPVNTFVAGFIGSPPMNFLDATITDDGFLDFGEFKLKLLQDQFEVLEEENMVGKEVIFGIRPEDVHDASFTHIDVPEENTVKATVDIIENLGGEKIVHLRRGNISFTAKFPKESKVREGDEVSVVFDMKKIHIFRKDTEKAIF 375
               SCOP domains d2d62a1 A:1-243 automated matches                                                                                                                                                                                                                  d2d62a2 A:244-304 automated matches                          d2d62a3 A:305-375 automated matches                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------2d62A02 A:249-295,A:359-375                    -----------------2d62A03 A:313-357                            -2d62A02           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee..eeeeeeeeeee....eeeee.....hhhhhhhhhhh.....eeeeee..eeeeehhhhee.hhhhhheee...........hhhhhhhhhhhh...hhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhhhhhh.eeeeee..eeeeeehhhhhhhh..hhhhhhhh.....eeeeeee....eee....eee.hhhhhhhhhhh.....eeeeeehhh.eee.hhh........eeeeeeeeeee...eeeeeeee..eeeeeeee.........eeeeee.hhhheeee.....eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d62 A   1 mIGmAEVKLINIWKRFGDVTAVKDLSLEIKDGEFLVLLGPSGCGKTTTLRmIAGLEEPTRGQIYIEDNLVADPEKGVFVPPKERDVAmVFQSYALYPHmTVYDNIAFPLKLRKVPKQEIDKRVREVAEmLGLTELLNRKPRELSGGQRQRVALGRAIIRRPKVFLmDEPLSNLDAKLRVKmRAELKKLQRQLGVTTIYVTHDQVEAmTmGDRIAVmNKGELQQVGTPDEVYYKPVNTFVAGFIGSPPmNFLDATITDDGFLDFGEFKLKLLQDQFEVLEEENmVGKEVIFGIRPEDVHDASFTHIDVPEENTVKATVDIIENLGGEKIVHLRRGNISFTAKFPKESKVREGDEVSVVFDmKKIHIFRKDTEKAIF 375
                            |  |    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  |    290       300       310       320       330       340       350       360       370     
                            |  |                                             51-MSE                               88-MSE     99-MSE                       129-MSE                              166-MSE        181-MSE                   207-MSE    |                             248-MSE                            283-MSE                                                                      360-MSE           
                            1-MSE                                                                                                                                                                                                         209-MSE  |                                                                                                                                                               
                               4-MSE                                                                                                                                                                                                             216-MSE

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 '\|'

Classification and Annotation

SCOP Domains (2, 3)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric Unit(hide GO term definitions)

Chain A (O57933_PYRHO | O57933)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0016820	hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	Catalysis of the hydrolysis of an acid anhydride to directly drive the transport of a substance across a membrane.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0043190	ATP-binding cassette (ABC) transporter complex	A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.

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