4I3G - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF DESR, A BETA-GLUCOSIDASE FROM STREPTOMYCES VENEZUELAE IN COMPLEX WITH D-GLUCOSE.

Authors :   M. W. Zmudka, H. M. Holden

Date :   26 Nov 12 (Deposition) - 20 Feb 13 (Release) - 28 Aug 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.40

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

Keywords :   Pa14 Domain, Beta-Glucosidase, Macrolide Antibiotic, Antibiotic Activation, Extracellular, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. W. Zmudka, J. B. Thoden, H. M. Holden
The Structure Of Desr From Streptomyces Venezuelae, A Beta-Glucosidase Involved In Macrolide Activation.
Protein Sci. V. 22 883 2013
PubMed-ID: 23225731 | Reference-DOI: 10.1002/PRO.2204

Molecule 1 - BETA-GLUCOSIDASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28
	Expression System Strain	:	ROSETTA2 (DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	DESR
	Organism Scientific	:	STREPTOMYCES VENEZUELAE
	Organism Taxid	:	54571

		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 (4, 20)

No.	Name	Count	Type	Full Name
1	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	MPO	2	Ligand/Ion	3[N-MORPHOLINO]PROPANE SULFONIC ACID
4	SO4	12	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 12)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	MPO	1	Ligand/Ion	3[N-MORPHOLINO]PROPANE SULFONIC ACID
4	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (4, 8)

No.	Name	Count	Type	Full Name
1	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	MPO	1	Ligand/Ion	3[N-MORPHOLINO]PROPANE SULFONIC ACID
4	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	VAL A:80 , ASP A:98 , ARG A:162 , LYS A:195 , HIS A:196 , ARG A:206 , MET A:238 , TYR A:241 , ASP A:273 , SER A:410 , GLU A:578 , HOH A:1344 , HOH A:1610	BINDING SITE FOR RESIDUE BGC A 901
02	AC2	SOFTWARE	GLN A:108 , ARG A:356 , LYS A:358	BINDING SITE FOR RESIDUE SO4 A 902
03	AC3	SOFTWARE	ARG A:377 , SER A:621 , HOH A:1585	BINDING SITE FOR RESIDUE SO4 A 903
04	AC4	SOFTWARE	GLY A:589 , THR A:590 , ASP A:592 , LYS A:593 , HOH A:1182 , HOH A:1554	BINDING SITE FOR RESIDUE SO4 A 904
05	AC5	SOFTWARE	ASP A:124 , ASP A:125 , THR A:126 , ARG A:176 , HOH A:1078 , HOH A:1525 , HOH A:1657	BINDING SITE FOR RESIDUE SO4 A 905
06	AC6	SOFTWARE	ALA A:661 , GLU A:662 , ASN A:663 , HOH A:1177 , HOH A:1777	BINDING SITE FOR RESIDUE SO4 A 906
07	AC7	SOFTWARE	GLY A:380 , GLN A:381 , ARG A:624 , HOH A:1012	BINDING SITE FOR RESIDUE SO4 A 907
08	AC8	SOFTWARE	LYS A:763 , LYS A:764 , HOH A:1110 , HOH A:1285 , HOH A:1343 , HOH A:1408 , HOH A:1438	BINDING SITE FOR RESIDUE SO4 A 908
09	AC9	SOFTWARE	ARG A:736 , HOH A:1272 , HOH A:1430 , ARG B:52	BINDING SITE FOR RESIDUE SO4 A 909
10	BC1	SOFTWARE	PHE A:207 , TRP A:274 , LEU A:275 , HOH A:1344	BINDING SITE FOR RESIDUE MPO A 910
11	BC2	SOFTWARE	ARG A:788 , THR A:803 , HOH A:1366	BINDING SITE FOR RESIDUE EDO A 911
12	BC3	SOFTWARE	THR A:726 , ASP A:787 , ARG A:788 , HOH A:1413 , HOH A:1530	BINDING SITE FOR RESIDUE EDO A 912
13	BC4	SOFTWARE	VAL B:80 , ASP B:98 , ARG B:162 , LYS B:195 , HIS B:196 , ARG B:206 , MET B:238 , TYR B:241 , ASP B:273 , SER B:410 , GLU B:578 , HOH B:1511	BINDING SITE FOR RESIDUE BGC B 901
14	BC5	SOFTWARE	ASP B:124 , ASP B:125 , THR B:126 , ARG B:176 , HOH B:1127 , HOH B:1302 , HOH B:1405	BINDING SITE FOR RESIDUE SO4 B 902
15	BC6	SOFTWARE	ARG A:736 , HOH A:1754 , ARG B:52 , HOH B:1169 , HOH B:1532	BINDING SITE FOR RESIDUE SO4 B 903
16	BC7	SOFTWARE	GLN B:108 , ARG B:356 , LYS B:358	BINDING SITE FOR RESIDUE SO4 B 904
17	BC8	SOFTWARE	ARG B:377 , SER B:621	BINDING SITE FOR RESIDUE SO4 B 905
18	BC9	SOFTWARE	PHE B:207 , TRP B:274 , LEU B:275 , HOH B:1511	BINDING SITE FOR RESIDUE MPO B 906
19	CC1	SOFTWARE	HIS B:412 , GLY B:511 , LYS B:512 , HOH B:1166 , HOH B:1676 , HOH B:1677	BINDING SITE FOR RESIDUE EDO B 907
20	CC2	SOFTWARE	ALA B:348 , THR B:349	BINDING SITE FOR RESIDUE EDO B 908

Asymmetric Unit

No.	Residues
1	A:239	-	A:250
2	B:239	-	B:250

Asymmetric Unit

No.	Residues
1	Asp A:98	-	Gly A:99
2	Gly A:149	-	Pro A:150
3	Lys A:195	-	His A:196
4	Phe A:197	-	Ala A:198
5	Leu A:383	-	Pro A:384
6	Ser A:454	-	Pro A:455
7	Tyr A:674	-	Pro A:675
8	Asp B:98	-	Gly B:99
9	Gly B:149	-	Pro B:150
10	Lys B:195	-	His B:196
11	Phe B:197	-	Ala B:198
12	Leu B:383	-	Pro B:384
13	Ser B:454	-	Pro B:455
14	Tyr B:674	-	Pro B:675

(no "SAP(SNP)/Variant" information available for 4I3G)

(no "PROSITE Motif" information available for 4I3G)

(no "Exon" information available for 4I3G)

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:778
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.............eee..hhhhh...eeee.................hhhhhhhh.hhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhhhhhhhhhhhhh....eeeee............eee.hhhhhhhh.hhhhhhhhhh...eeee...ee..ee...hhhhhh...........eeeeee....hhhhhhhh..eee....................hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhheeeee.......hhhhh.eeeee.hhhh..................hhhhhhhhhhh...eeeee.......ee.hhh.ee.....eeee....eeeeeeeeeee...eeeeeeeeee.eeeeeee..eeeeehhhhh.....eeee..eeeeeeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee................hhhhhhhhhhhhh..eeeeee........hhhhh.eeee......hhhhhhhhhhh..................................eee.......hhhhhhhhh...............eee...eeee.....eeeeeeeee.....eeeeeeeeee...........eeeeeeeeeee....eeeeeeeehhhh.eeee....eeee..eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3g A  51 SRAAELVAQMTLDEKISFVHWALDPDRQNVGYLPGVPRLGIPELRAADGPNGIRLVGQTATALPAPVALASTFDDTMADSYGKVMGRDGRALNQDMVLGPMMNNIRVPHGGRNYETFSEDPLVSSRTAVAQIKGIQGAGLMTTAKHFAANNQENNRFSVNANVDEQTLREIEFPAFEASSKAGAASFMCAYNGLNGKPSCGNDELLNNVLRTQWGFQGWVMSDWLATPGTDAITKGLDQEMGVELPGDVPKGEPSPPAKFFGEALKTAVLNGTVPEAAVTRSAERIVGQMEKFGLLLATPAPRPERDKAGAQAVSRKVAENGAVLLRNEGQALPLAGDAGKSIAVIGPTAVDPKVTGLGSAHVVPDSAAAPLDTIKARAGAGATVTYETGEETFGTQIPAGNLSPAFNQGHQLEPGKAGALYDGTLTVPADGEYRIAVRATGGYATVQLGSHTIEAGQVYGKVSSPLLKLTKGTHKLTISGFAMSATPLSLELGWVTPAAADATIAEAVKSARKARTAVVFAYDDGTEGVDRPNLSLPGTQDKLISAVADANPNTIVVLNTGSSVLMPWLSKTRAVLDMWYPGQAGAEATAALLYGDVNPSGKLTQSFPAAENQHAVAGDPTSYPGVDNQQTYREGIHVGYRWFDKENVKPLFPFGHGLSYTSFTQSAPTVVRTSTGGLKVTVTVRNSGKRAGQEVVQAYLGASPNVTAPQAKKKLVGYTKVSLAAGEAKTVTVNVDRRQLQFWDAATDNWKTGTGNRLLQTGSSSADLRGSATVNVW 828
                                    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       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820

Chain B from PDB  Type:PROTEIN  Length:780
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh.hhhhhhh.............eee..hhhhh...eeee.................hhhhhhh..hhhhhhhhhhhhhhhhhhh...ee..............hhhhh...hhhhhhhhhhhhhhhhhhh....eeeee............eee.hhhhhhhhhhhhhhhhhhh...eeee...ee..ee...hhhhhh...........eeeeee....hhhhhhh...eee....................hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhheeeee.......hhhhh.eeeee.hhhh..................hhhhhhhhhhh...eeeee.......ee.hhh.ee.....eeee....eeeeeeeeeee...eeeeeeeeee.eeeeeee..eeeeehhhhh.....eeee..eeeeeeeeeee.....eeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeeee................hhhhhhhhhhhhh..eeeeee........hhhhh.eeee......hhhhhhhhhhh..................................eee.......hhhhhhhhh...............eee...eeee.....eeeeeeeee.....eeeeeeeeee...........eeeeeeeeeee....eeeeeeeehhhh.eeee....eeee..eeeeeeee.......eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4i3g B  49 YTSRAAELVAQMTLDEKISFVHWALDPDRQNVGYLPGVPRLGIPELRAADGPNGIRLVGQTATALPAPVALASTFDDTMADSYGKVMGRDGRALNQDMVLGPMMNNIRVPHGGRNYETFSEDPLVSSRTAVAQIKGIQGAGLMTTAKHFAANNQENNRFSVNANVDEQTLREIEFPAFEASSKAGAASFMCAYNGLNGKPSCGNDELLNNVLRTQWGFQGWVMSDWLATPGTDAITKGLDQEMGVELPGDVPKGEPSPPAKFFGEALKTAVLNGTVPEAAVTRSAERIVGQMEKFGLLLATPAPRPERDKAGAQAVSRKVAENGAVLLRNEGQALPLAGDAGKSIAVIGPTAVDPKVTGLGSAHVVPDSAAAPLDTIKARAGAGATVTYETGEETFGTQIPAGNLSPAFNQGHQLEPGKAGALYDGTLTVPADGEYRIAVRATGGYATVQLGSHTIEAGQVYGKVSSPLLKLTKGTHKLTISGFAMSATPLSLELGWVTPAAADATIAEAVKSARKARTAVVFAYDDGTEGVDRPNLSLPGTQDKLISAVADANPNTIVVLNTGSSVLMPWLSKTRAVLDMWYPGQAGAEATAALLYGDVNPSGKLTQSFPAAENQHAVAGDPTSYPGVDNQQTYREGIHVGYRWFDKENVKPLFPFGHGLSYTSFTQSAPTVVRTSTGGLKVTVTVRNSGKRAGQEVVQAYLGASPNVTAPQAKKKLVGYTKVSLAAGEAKTVTVNVDRRQLQFWDAATDNWKTGTGNRLLQTGSSSADLRGSATVNVW 828
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778       788       798       808       818       828

Legend:		→ Mismatch	(orange background)
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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 '\|'

(no "SCOP Domain" information available for 4I3G)

(no "CATH Domain" information available for 4I3G)

(no "Pfam Domain" information available for 4I3G)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Cis Peptide Bonds
		Asp A:98 - Gly A:99	[ RasMol ]
		Asp B:98 - Gly B:99	[ RasMol ]
		Gly A:149 - Pro A:150	[ RasMol ]
		Gly B:149 - Pro B:150	[ RasMol ]
		Leu A:383 - Pro A:384	[ RasMol ]
		Leu B:383 - Pro B:384	[ RasMol ]
		Lys A:195 - His A:196	[ RasMol ]
		Lys B:195 - His B:196	[ RasMol ]
		Phe A:197 - Ala A:198	[ RasMol ]
		Phe B:197 - Ala B:198	[ RasMol ]
		Ser A:454 - Pro A:455	[ RasMol ]
		Ser B:454 - Pro B:455	[ RasMol ]
		Tyr A:674 - Pro A:675	[ RasMol ]
		Tyr B:674 - Pro B:675	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (4, 20)

Sites (20, 20)

SS Bonds (2, 2)

Cis Peptide Bonds (14, 14)

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