5J14 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ENDOGLYCOCERAMIDASE I FROM RHODOCOC-CUS EQUI IN COMPLEX WITH GM3

Authors :   L. Chen

Date :   28 Mar 16 (Deposition) - 27 Apr 16 (Release) - 05 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.92

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

Keywords :   Complex, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. B. Han, L. Q. Chen, Z. Li, Y. M. Tan, Y. Feng, G. Y. Yang
Structural Insights Into The Broad Substrate Specificity Of A Novel Endoglycoceramidase I Belonging To A New Subfamily Of Gh5 Glycosidases
J. Biol. Chem. V. 292 4789 2017
PubMed-ID: 28179425 | Reference-DOI: 10.1074/JBC.M116.763821

Molecule 1 - PUTATIVE SECRETED ENDOGLYCOSYLCERAMIDASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
	Expression System Strain	:	BL21-GOLD(DE3)PLYSS AG
	Expression System Taxid	:	866768
	Expression System Vector Type	:	PLASMID
	Gene	:	REQ_38260
	Mutation	:	YES
	Organism Scientific	:	RHODOCOCCUS EQUI 103S
	Organism Taxid	:	685727
	Strain	:	103S

		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 (5, 9)

No.	Name	Count	Type	Full Name
1	18C	2	Ligand/Ion	N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE
2	BGC	2	Ligand/Ion	BETA-D-GLUCOSE
3	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
4	NA	2	Ligand/Ion	SODIUM ION
5	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	18C	1	Ligand/Ion	N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE
2	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	NA	-1	Ligand/Ion	SODIUM ION
5	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 2 (3, 3)

No.	Name	Count	Type	Full Name
1	18C	1	Ligand/Ion	N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)STEARAMIDE
2	BGC	1	Ligand/Ion	BETA-D-GLUCOSE
3	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
4	NA	-1	Ligand/Ion	SODIUM ION
5	SIA	-1	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:60 , ASP A:62 , PRO A:64 , HOH A:746 , HOH A:840 , HOH A:906	binding site for residue NA A 504
2	AC2	SOFTWARE	ASP B:60 , ASP B:62 , PRO B:64 , HOH B:873 , HOH B:879 , HOH B:898	binding site for residue NA B 503
3	AC3	SOFTWARE	LYS A:61 , HIS A:131 , ASP A:133 , PHE A:162 , PRO A:163 , TYR A:166 , ASN A:213 , GLU A:214 , TRP A:216 , PHE A:225 , VAL A:262 , ASN A:265 , GLN A:266 , MET A:267 , TYR A:293 , ILE A:295 , GLN A:298 , LEU A:299 , TYR A:302 , ASP A:342 , TRP A:365 , HOH A:640 , HOH A:699 , HOH A:768 , HOH A:774 , HOH A:872 , 18C B:504	binding site for Poly-Saccharide residues BGC A 501 through 18C A 505
4	AC4	SOFTWARE	ASP A:60 , LYS A:61 , ASP A:62 , PRO A:64 , HIS A:131 , ASP A:133 , PHE A:162 , ASN A:213 , GLU A:214 , TYR A:293 , GLN A:298 , TYR A:302 , LEU A:305 , ASP A:342 , TRP A:365 , 18C A:505 , HOH A:640 , HOH A:699 , HOH A:746 , HOH A:768 , HOH A:774 , HOH A:840 , HOH A:906 , ASP B:60 , LYS B:61 , ASP B:62 , PRO B:64 , HIS B:131 , ASP B:133 , PHE B:162 , PRO B:163 , ASN B:213 , GLU B:214 , PHE B:225 , ASN B:265 , MET B:267 , TYR B:293 , ILE B:295 , GLN B:298 , ASP B:342 , TRP B:365 , HOH B:618 , HOH B:686 , HOH B:728 , HOH B:808 , HOH B:821 , HOH B:845 , HOH B:873 , HOH B:879 , HOH B:898	binding site for Poly-Saccharide residues BGC B 501 through 18C B 504

Asymmetric Unit

No.	Residues
1	A:224	-	A:229
2	A:294	-	A:313
3	B:224	-	B:229
4	B:294	-	B:313

Asymmetric Unit

No.	Residues
1	Ala A:63	-	Pro A:64
2	Phe A:162	-	Pro A:163
3	Phe A:225	-	Pro A:226
4	Pro A:275	-	Pro A:276
5	Trp A:365	-	His A:366
6	Ala B:63	-	Pro B:64
7	Phe B:162	-	Pro B:163
8	Phe B:225	-	Pro B:226
9	Pro B:275	-	Pro B:276
10	Trp B:365	-	His B:366

(no "SAP(SNP)/Variant" information available for 5J14)

(no "PROSITE Motif" information available for 5J14)

(no "Exon" information available for 5J14)

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:450
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eee..eee.....ee..eeeee..............hhhhhhhhhhh...eeeeeehhhhhh......hhhhhhhhhhhhhhhhhh..eeeeee.....hhhhh....hhhhh.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeee.........hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhh..................eee..ee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.ee......hhhhhhhhhhhhh.eeee.............hhhhhhhh..eeeee.eeeeeeee......eeeeeee......eeee..........eeeee.eee.......eeeeee.....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j14 A  29 PATPITTLQADGTHLVDGYGRTVLLHGVNNVDKDAPYLPAGETLTPQDIDILVRHGFNTVRLGTSFDALMPQRGQIDEAYLDRLTGVVDALTARGMHVLLDNHQDGLSKAWGGNGFPEWAIESRPREWEPNPGFPLYYLMPSLNAGWDEVWGNTHGALDHLGTALGALAERVEGKPGVMGIELLNEPWPGSRFLSCFPNGCPDFDRTYQAAMQKLTDAVRAQNPTIPVYWEPNVTWNQMMPSNLFAPPVTPALTTADVVFAPHDYCIPSQLAIYLGLPQALRGLCVPQQDLTWSNIDAITERANVPTVITSFGDGDPTVLKNTLARADERFIGWQYWHFGAGNATDPFLGEVGRQLVRTYPQATAGEPGRMIFDADNGDFAYRFTPRAATRPTEIFVSDLHYPDGYAVQVDGGQVTSAPGARIVTVVADGSGPVTVKINRPGSAGAEVPD 478
                                    38        48        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

Chain B from PDB  Type:PROTEIN  Length:434
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eee.....ee..eeeee..............hhhhhhhhhhh...eeeeeehhhhhh......hhhhhhhhhhhhhhhhhh..eeeeee.....hhhhh....hhhhh.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhh..................eee..ee.......hhhhhhhhhhhhhhhhhhhh...ee.ee......hhhhhhhhhhhh..eeee.............hhhhhhhh..eeeee.eeeeeeee......eeeeeee......eeee..........eeeee.eee.......eeeeee.....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j14 B  31 TPITTLQADGTHLVDGYGRTVLLHGVNNVDKDAPYLPAGETLTPQDIDILVRHGFNTVRLGTSFDALMPQRGQIDEAYLDRLTGVVDALTARGMHVLLDNHQDGLSKAWGGNGFPEWAIESRPREWEPNPGFPLYYLMPSLNAGWDEVWGNTHGALDHLGTALGALAERVEGKPGVMGIELLNEPWPGSRFLSCFPNGCPDFDRTYQAAMQKLTDAVRAQNPTIPVYWEPNVTWNQMMPSNLFAPPVTPALTTADVVFAPHDYCIPSQLCVPQQDLTWSNIDAITERANVPTVITSFGDGDPTVLKNTLARADERFIGWQYWHFGAGNATDPFLGEVGRQLVRTYPQATAGEPGRMIFDADNGDFAYRFTPRAATRPTEIFVSDLHYPDGYAVQVDGGQVTSAPGARIVTVVADGSGPVTVKINRPGSAGAEVP 477
                                    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       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473    
                                                                                                                                                                                                                                                                                                     298|                                                                                                                                                                     
                                                                                                                                                                                                                                                                                                      312

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 5J14)

(no "CATH Domain" information available for 5J14)

(no "Pfam Domain" information available for 5J14)

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ala A:63 - Pro A:64	[ RasMol ]
		Ala B:63 - Pro B:64	[ RasMol ]
		Phe A:162 - Pro A:163	[ RasMol ]
		Phe A:225 - Pro A:226	[ RasMol ]
		Phe B:162 - Pro B:163	[ RasMol ]
		Phe B:225 - Pro B:226	[ RasMol ]
		Pro A:275 - Pro A:276	[ RasMol ]
		Pro B:275 - Pro B:276	[ RasMol ]
		Trp A:365 - His A:366	[ RasMol ]
		Trp B:365 - His B:366	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (4, 4)

SS Bonds (4, 4)

Cis Peptide Bonds (10, 10)

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