3N4A - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF D-XYLOSE ISOMERASE IN COMPLEX WITH S-1,2-PROPANDIOL

Authors :   J. Behnen, A. Heine, G. Klebe

Date :   21 May 10 (Deposition) - 25 May 11 (Release) - 15 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.94

Chains :   Asym. Unit : A
Biol. Unit 1: A  (4x)

Keywords :   Isomerase, Intramolecular Oxidoreductse, S-1, 2-Propandiol, Tim Barrel-Beta-Alpha-Barrels, Two Metal Binding Ites, Manganese (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Behnen, H. Koster, G. Neudert, T. Craan, A. Heine, G. Klebe
Experimental And Computational Active Site Mapping As A Starting Point To Fragment-Based Lead Discovery.
Chemmedchem V. 7 248 2012
PubMed-ID: 22213702 | Reference-DOI: 10.1002/CMDC.201100490

Molecule 1 - XYLOSE ISOMERASE
	Chains	:	A
	EC Number	:	5.3.1.5
	Organism Scientific	:	STREPTOMYCES RUBIGINOSUS
	Organism Taxid	:	1929

		1
Asymmetric Unit	:	A
Biological Unit 1 (4x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MN	2	Ligand/Ion	MANGANESE (II) ION
3	PGO	1	Ligand/Ion	S-1,2-PROPANEDIOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	PGO	4	Ligand/Ion	S-1,2-PROPANEDIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:216 , HIS A:219 , ASP A:254 , ASP A:256 , HOH A:2350	BINDING SITE FOR RESIDUE MN A 701
2	AC2	SOFTWARE	GLU A:180 , GLU A:216 , ASP A:244 , ASP A:286 , PGO A:601 , HOH A:2133	BINDING SITE FOR RESIDUE MN A 801
3	AC3	SOFTWARE	GLN A:233 , HOH A:2184	BINDING SITE FOR RESIDUE CL A 501
4	AC4	SOFTWARE	HIS A:53 , TRP A:136 , GLU A:180 , ASP A:244 , ASP A:286 , MN A:801 , HOH A:2079 , HOH A:2133 , HOH A:2138	BINDING SITE FOR RESIDUE PGO A 601

(no "SS Bond" information available for 3N4A)

Asymmetric Unit

No.	Residues
1	Glu A:185	-	Pro A:186

(no "SAP(SNP)/Variant" information available for 3N4A)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XYLOSE_ISOMERASE	PS51415	Xylose isomerase family profile.	XYLA_STRRU	4-383	1	A:3-382

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	XYLOSE_ISOMERASE	PS51415	Xylose isomerase family profile.	XYLA_STRRU	4-383	4	A:3-382

(no "Exon" information available for 3N4A)

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:386
 aligned with XYLA_STRRU | P24300 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381      
           XYLA_STRRU     2 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 387
               SCOP domains d3n4aa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------AP_endonuc_2-3n4aA01 A:39-264                                                                                                                                                                                                     -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhh.eeeehhhhh...............hhhhhhhhhhhhh..eeeeehhhhh....hhhhhhhhhhhhhhhhhhhh....eee.....hhhhh.......hhhhhhhhhhhhhhhhhhhhhh...eeee.....ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee.........ee...hhhhhhhhhh...hhh.eee..hhhhhhh...hhhhhhhhhhhhh.....ee.................hhhhhhhhhhhhhhh.....eee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --XYLOSE_ISOMERASE  PDB: A:3-382 UniProt: 4-383                                                                                                                                                                                                                                                                                                                                               ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3n4a A   1 NYQPTPEDRFTFGLWTVGWQGRDPFGDATRRALDPVESVRRLAELGAHGVTFHDDDLIPFGSSDSEREEHVKRFRQALDDTGMKVPMATTNLFTHPVFKDGGFTANDRDVRRYALRKTIRNIDLAVELGAETYVAWGGREGAESGGAKDVRDALDRMKEAFDLLGEYVTSQGYDIRFAIEPKPNEPRGDILLPTVGHALAFIERLERPELYGVNPEVGHEQMAGLNFPHGIAQALWAGKLFHIDLNGQNGIKYDQDLRFGAGDLRAAFWLVDLLESAGYSGPRHFDFKPPRTEDFDGVWASAAGCMRNYLILKERAAAFRADPEVQEALRASRLDELARPTAADGLQALLDDRSAFEEFDVDAAAARGMAFERLDQLAMDHLLGAR 386
                                    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       380

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Xylose isomerase-like (125)

Family: Xylose isomerase (97)

Protein domain: automated matches (15)

Streptomyces rubiginosus [TaxId: 1929] (15)

d3n4aa_

(no "CATH Domain" information available for 3N4A)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: AP_endonuc_2 (72)

Streptomyces rubiginosus (22)

AP_endonuc_2-3n4aA01

A:39-264

Asymmetric Unit(hide GO term definitions)

Chain A (XYLA_STRRU | P24300)

molecular function
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0009045	xylose isomerase activity	Catalysis of the reaction: D-xylose = D-xylulose.
biological process
	GO:0042732	D-xylose metabolic process	The chemical reactions and pathways involving D-xylose, a naturally occurring plant polysaccharide.
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006098	pentose-phosphate shunt	The glucose-6-phosphate catabolic process in which, coupled to NADPH synthesis, glucose-6-P is oxidized with the formation of carbon dioxide (CO2) and ribulose 5-phosphate; ribulose 5-P then enters a series of reactions interconverting sugar phosphates. The pentose phosphate pathway is a major source of reducing equivalents for biosynthesis reactions and is also important for the conversion of hexoses to pentoses.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:185 - Pro A:186	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	3n4a
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(no "Related Entries Specified in the PDB File" available for 3N4A)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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