5BXR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   LNBASE IN COMPLEX WITH LNB-NHACDNJ

Authors :   T. Ito, T. Arakawa, S. Fushinobu

Date :   09 Jun 15 (Deposition) - 09 Sep 15 (Release) - 14 Oct 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

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

Keywords :   Tim Barrel, Hydrolase, Distal Gut, Human Milk Oligosaccharides, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hattie, T. Ito, A. W. Debowski, T. Arakawa, T. Katayama, K. Yamamoto S. Fushinobu, K. A. Stubbs
Gaining Insight Into The Catalysis By Gh20 Lacto-N-Biosidas Using Small Molecule Inhibitors And Structural Analysis
Chem. Commun. (Camb. ) V. 51 15008 2015
PubMed-ID: 26312778 | Reference-DOI: 10.1039/C5CC05494J
(for further references see the PDB file header)

Molecule 1 - LACTO-N-BIOSIDASE
	Chains	:	A, B
	EC Number	:	3.2.1.140
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21 CODON PLUS
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 41-644
	Gene	:	LNBB
	Organism Scientific	:	BIFIDOBACTERIUM BIFIDUM JCM 1254
	Organism Taxid	:	398514

		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 (3, 9)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	NOK	2	Ligand/Ion	2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
3	SO4	5	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NOK	1	Ligand/Ion	2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NOK	1	Ligand/Ion	2-ACETAMIDO-1,2-DIDEOXYNOJIRMYCIN
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:146 , ASP A:147 , HOH A:805 , HOH A:927	binding site for residue SO4 A 703
2	AC2	SOFTWARE	GLN A:190 , ASN A:265 , ASN A:286 , HOH A:816 , HOH A:891 , HOH A:1080	binding site for residue SO4 A 704
3	AC3	SOFTWARE	SER A:423 , ALA A:424 , GLN A:425 , VAL A:426 , PHE A:471 , ARG A:599 , HOH A:916 , HOH A:932 , HOH A:947	binding site for residue SO4 A 705
4	AC4	SOFTWARE	GLN B:190 , ASN B:265 , ASN B:286 , HOH B:852 , HOH B:858 , HOH B:1069	binding site for residue SO4 B 703
5	AC5	SOFTWARE	SER B:423 , ALA B:424 , GLN B:425 , VAL B:426 , PHE B:471 , ARG B:599 , HOH B:880 , HOH B:1029 , HOH B:1122	binding site for residue SO4 B 704
6	AC6	SOFTWARE	GLN A:190 , GLU A:216 , ASN A:259 , HIS A:263 , ASP A:320 , GLU A:321 , TRP A:373 , TRP A:394 , TYR A:419 , TYR A:427 , TRP A:465 , PRO A:466 , ASP A:467 , HOH A:856 , HOH A:998 , HOH A:1029 , HOH A:1036 , HOH A:1080 , HOH A:1106	binding site for Poly-Saccharide residues GAL A 701 through NOK A 702
7	AC7	SOFTWARE	GLN B:190 , GLU B:216 , ASN B:259 , HIS B:263 , ASP B:320 , GLU B:321 , TRP B:373 , TRP B:394 , TYR B:419 , TYR B:427 , TRP B:465 , PRO B:466 , ASP B:467 , HOH B:831 , HOH B:876 , HOH B:1030 , HOH B:1046 , HOH B:1069 , HOH B:1118	binding site for Poly-Saccharide residues GAL B 701 through NOK B 702

Asymmetric Unit

No.	Residues
1	A:187	-	A:189
2	A:564	-	A:589
3	B:187	-	B:189
4	B:564	-	B:589

Asymmetric Unit

No.	Residues
1	Val A:56	-	Pro A:57
2	Trp A:232	-	Ser A:233
3	Ser A:260	-	Pro A:261
4	Gly A:542	-	Pro A:543
5	Lys A:616	-	Asp A:617
6	Val B:56	-	Pro B:57
7	Gly B:107	-	Ser B:108
8	Trp B:232	-	Ser B:233
9	Ser B:260	-	Pro B:261
10	Gly B:542	-	Pro B:543

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

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

(no "Exon" information available for 5BXR)

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:634
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee.....eee...................eeeeeeee.....eeee...hhhhhhhhhhhhhhhhh...eee........eeeee...hhhhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhhh...eeeee.........hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhh.hhh.eee.....eeeeee...hhhhhhhhhhhhhhhhh.....eeeee........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeee................eeee......hhhhhhhh...eee.hhh.eee........hhhhhhhh.....ee...ee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhh........eeeehhhhh......eeeee.....eeeee.....eee.....ee..ee.......eee..........hhhhhhhhhh..eeeee.....eeeee.....eeee......hhhhhh.......eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxr A  30 SSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQRLAIATGNEQNIDLETHRPAAGTVAQFPADLVSD 663
                                    39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659

Chain B from PDB  Type:PROTEIN  Length:636
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......ee.....eee...................eeeeeeee.....eeee...hhhhhhhhhhhhhhhhh...eeee.......eeeee...hhhhhh...eeeeee..eeeeee.hhhhhhhhhhhhhhhhh....eeeeeeeee.....eeeeeee......hhhhhhhhhhhhhhh...eeeee.........hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhh.hhh.eee.....eeeeee...hhhhhhhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeee................eeee......hhhhhhhh...eee.hhh.eee........hhhhhhhh.....ee...ee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhh.......eeeehhhhh......eeeee.....eeeee.....eee.....ee..ee.......eee..........hhhhhhhhhh..eeeee.....eeeee.....eeee......hhhhhhh......eeeehhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5bxr B  28 HHSSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQRLAIATGNEQNIDLETHRPAAGTVAQFPADLVSD 663
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657

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 5BXR)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NOK	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
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		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gly A:542 - Pro A:543	[ RasMol ]
		Gly B:107 - Ser B:108	[ RasMol ]
		Gly B:542 - Pro B:543	[ RasMol ]
		Lys A:616 - Asp A:617	[ RasMol ]
		Ser A:260 - Pro A:261	[ RasMol ]
		Ser B:260 - Pro B:261	[ RasMol ]
		Trp A:232 - Ser A:233	[ RasMol ]
		Trp B:232 - Ser B:233	[ RasMol ]
		Val A:56 - Pro A:57	[ RasMol ]
		Val B:56 - Pro B:57	[ RasMol ]

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

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 9)

Sites (7, 7)

SS Bonds (4, 4)

Cis Peptide Bonds (10, 10)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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