5J7Z - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ENDOGLYCOCERAMIDASE I FROM RHODOCOC-CUS EQUI IN COMPLEX WITH GM1

Authors :   L. Chen

Date :   07 Apr 16 (Deposition) - 27 Apr 16 (Release) - 05 Apr 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.15

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 (6, 8)

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	2	Ligand/Ion	BETA-D-GALACTOSE
4	NA	2	Ligand/Ion	SODIUM ION
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (5, 6)

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	2	Ligand/Ion	BETA-D-GALACTOSE
4	NA	-1	Ligand/Ion	SODIUM ION
5	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	1	Ligand/Ion	O-SIALIC ACID

Biological Unit 2 (0, 0)

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	NGA	-1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE
6	SIA	-1	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:60 , ASP A:62 , PRO A:64 , HOH A:862	binding site for residue NA A 606
2	AC2	SOFTWARE	ASP B:60 , ASP B:62 , PRO B:64	binding site for residue NA B 501
3	AC3	SOFTWARE	LYS A:61 , ASP A:62 , HIS A:131 , ASP A:133 , PHE A:162 , PRO A:163 , TYR A:166 , ASN A:213 , GLU A:214 , TRP A:216 , VAL A:262 , ASN A:265 , GLN A:266 , TYR A:293 , GLN A:298 , ILE A:301 , TYR A:302 , ASP A:342 , TRP A:365 , HOH A:730 , HOH A:788 , HOH A:795 , HOH A:817 , HOH A:827 , HOH A:844	binding site for Poly-Saccharide residues GAL A 601 through 18C A 607

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 5J7Z)

(no "PROSITE Motif" information available for 5J7Z)

(no "Exon" information available for 5J7Z)

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......hhhhhhhhhhhhhhhhh...eeeeee.....hhhhh....hhhhh.............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhh..................eee.....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee.........hhhhhhhhhhhhh.eeee.............hhhhhhhh..eeeee.eeeeeeee......eeeeeee......eeee..........eeeee.eee.......eeeeee.....eeeeee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j7z 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:436
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               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...hhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh....eee..hhhhhhh..................eee..ee........hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhh..eeee.............hhhhhhhh..eeeee.eeeeeeee......eeeeeee......eeee..........eeeee.eee.......eeeeee.....eeeeee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j7z B  29 PATPITTLQADGTHLVDGYGRTVLLHGVNNVDKDAPYLPAGETLTPQDIDILVRHGFNTVRLGTSFDALMPQRGQIDEAYLDRLTGVVDALTARGMHVLLDNHQDGLSKAWGGNGFPEWAIESRPREWEPNPGFPLYYLMPSLNAGWDEVWGNTHGALDHLGTALGALAERVEGKPGVMGIELLNEPWPGSRFLSCFPNGCPDFDRTYQAAMQKLTDAVRAQNPTIPVYWEPNVTWNQMMPSNLFAPPVTPALTTADVVFAPHDYCIPSQLCVPQQDLTWSNIDAITERANVPTVITSFGDGDPTVLKNTLARADERFIGWQYWHFGAGNATDPFLGEVGRQLVRTYPQATAGEPGRMIFDADNGDFAYRFTPRAATRPTEIFVSDLHYPDGYAVQVDGGQVTSAPGARIVTVVADGSGPVTVKINRPGSAGAEVP 477
                                    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||     321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471      
                                                                                                                                                                                                                                                                                                        299|                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                         313

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 5J7Z)

(no "CATH Domain" information available for 5J7Z)

(no "Pfam Domain" information available for 5J7Z)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		18C	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BGC	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NGA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SIA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ 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 ]

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

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	5j7z
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	E4W8N9_RHOE1 \| E4W8N9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	E4W8N9_RHOE1 \| E4W8N9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	E4W8N9_RHOE1 \| E4W8N9	:	5ccu 5j14

5ccu	THE WILD TYPE PROTEIN
5j14

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File