4H04 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   LACTO-N-BIOSIDASE FROM BIFIDOBACTERIUM BIFIDUM

Authors :   T. Ito, T. Katayama, J. Wada, R. Suzuki, H. Ashida, T. Wakagi, K. Yamamot S. Fushinobu

Date :   07 Sep 12 (Deposition) - 20 Mar 13 (Release) - 10 Jul 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   Tim Barrel, Hydrolase, Extracellular (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Ito, T. Katayama, M. Hattie, H. Sakurama, J. Wada, R. Suzuki, H. Ashida, T. Wakagi, K. Yamamoto, K. A. Stubbs, S. Fushinobu
Crystal Structures Of A Glycoside Hydrolase Family 20 Lacto-N-Biosidase From Bifidobacterium Bifidum
J. Biol. Chem. V. 288 11795 2013
PubMed-ID: 23479733 | Reference-DOI: 10.1074/JBC.M112.420109
(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 CODONPLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	GH20 DOMAIN, UNP RESIDUES 41-663
	Gene	:	LNBB
	Organism Scientific	:	BIFIDOBACTERIUM BIFIDUM
	Organism Taxid	:	398514
	Strain	:	JCM1254

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	GAL	1	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 12)

No.	Name	Count	Type	Full Name
1	GAL	2	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SO4	8	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:423 , ALA A:424 , GLN A:425 , VAL A:426 , PHE A:471 , ARG A:599 , HOH A:801 , HOH A:914 , HOH A:1451	BINDING SITE FOR RESIDUE SO4 A 703
02	AC2	SOFTWARE	THR A:146 , ASP A:147 , HOH A:880 , HOH A:961 , HOH A:1184 , HOH A:1204 , HOH A:1251 , HOH A:1447	BINDING SITE FOR RESIDUE SO4 A 704
03	AC3	SOFTWARE	ARG A:587 , HOH A:1145	BINDING SITE FOR RESIDUE SO4 A 705
04	AC4	SOFTWARE	GLN A:190 , ASN A:265 , ASN A:286 , HOH A:821 , HOH A:989 , HOH A:1021 , HOH A:1428	BINDING SITE FOR RESIDUE SO4 A 706
05	AC5	SOFTWARE	SER B:423 , ALA B:424 , GLN B:425 , VAL B:426 , PHE B:471 , ARG B:599 , HOH B:801 , HOH B:1158 , HOH B:1301 , HOH B:1318	BINDING SITE FOR RESIDUE SO4 B 703
06	AC6	SOFTWARE	ALA B:397 , GLY B:398 , ARG B:587 , HOH B:1344	BINDING SITE FOR RESIDUE SO4 B 704
07	AC7	SOFTWARE	GLN B:190 , ASN B:265 , ASN B:286 , HOH B:882 , HOH B:959 , HOH B:1083 , HOH B:1163 , HOH B:1169	BINDING SITE FOR RESIDUE SO4 B 705
08	AC8	SOFTWARE	LYS B:400 , ARG B:448 , ASN B:588	BINDING SITE FOR RESIDUE SO4 B 706
09	AC9	SOFTWARE	GLN A:190 , GLU A:216 , ASN A:259 , HIS A:263 , ASP A:320 , GLU A:321 , TRP A:394 , TYR A:419 , TYR A:427 , TRP A:465 , PRO A:466 , ASP A:467 , HOH A:830 , HOH A:848 , HOH A:920 , HOH A:981 , HOH A:989 , HOH A:1064	BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 701 TO 702
10	BC1	SOFTWARE	GLN B:190 , GLU B:216 , ASN B:259 , HIS B:263 , ASP B:320 , GLU B:321 , TRP B:394 , TYR B:419 , TYR B:427 , TRP B:465 , PRO B:466 , ASP B:467 , HOH B:880 , HOH B:895 , HOH B:927 , HOH B:1055 , HOH B:1058 , HOH B:1083	BINDING SITE FOR DI-SACCHARIDE NAG B 701 AND GAL B 702

Asymmetric Unit

No.	Residues
1	A:564	-	A:589
2	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:398	-	Arg A:399
5	Gly A:542	-	Pro A:543
6	Lys A:616	-	Asp A:617
7	Val B:56	-	Pro B:57
8	Gly B:107	-	Ser B:108
9	Trp B:232	-	Ser B:233
10	Ser B:260	-	Pro B:261
11	Gly B:542	-	Pro B:543

(no "SAP(SNP)/Variant" information available for 4H04)

(no "PROSITE Motif" information available for 4H04)

(no "Exon" information available for 4H04)

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:633
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               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.....eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee........hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhh.hhh.eee.....eeeeee...hhhhhhhhhhhhhhhhh.....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
                 4h04 A  30 SSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQRLAIATGNEQNIDLETHRPAAGTVAQFPADLVS 662
                                    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:632
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               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.....eeeeeeee.....hhhhhhhhhhhhhhh...eeeeee........hhhhh.....hhhhhhhhhhhhhhh..eeeeeeee...hhhhhh.hhh.eee.....eeeeee...hhhhhhhhhhhhhhhh......eeeee........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...eeeee................eeee......hhhhhhhh...eee.hhh.eee........hhhhhhhh.....ee...ee.......eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhh........eeeehhhhh......eeeee.....eeeee.....eee.....ee..ee.......eee..........hhhhhhhhhhh.eeeee.....eeeee.....eeee......hhhhhhh......eeeehhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h04 B  30 SSGLVPRGSHMGYSATAPVNLTRPATVPSMDGWTDGTGAWTLGEGTRVVSSDALAARAQSLASELTKFTDVDIKAATGSATGKDISLTLDASKKAELGDEGFKLNIGSKGLEVIGATDIGVFYGTRSVSQMLRQGQLTLPAGTVATKPKYKERGATLCACQINISTDWIDRFLSDMADLRLNYVLLEMKLKPEEDNTKKAATWSYYTRDDVKKFVKKANNYGIDVIPEINSPGHMNVWLENYPEYQLADNSGRKDPNKLDISNPEAVKFYKTLIDEYDGVFTTKYWHMGADEYMIGTSFDNYSKLKTFAEKQYGAGATPNDAFTGFINDIDKYVKAKGKQLRIWNDGIVNTKNVSLNKDIVIEYWYGAGRKPQELVQDGYTLMNATQALYWSRSAQVYKVNAARLYNNNWNVGTFDGGRQIDKNYDKLTGAKVSIWPDSSYFQTENEVEKEIFDGMRFISQMTWSDSRPWATWNDMKADIDKIGYPLDIREYDYTPVDAGIYDIPQLKSISKGPWELITTPDGYYQMKDTVSGKCLALFTGSKHLDVVTQVGARPELRNCADVSVGQDQRNTANERNTQKWQIRADKDGKYTISPALTQQRLAIATGNEQNIDLETHRPAAGTVAQFPADLV 661
                                    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

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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 4H04)

(no "CATH Domain" information available for 4H04)

(no "Pfam Domain" information available for 4H04)

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	Cis Peptide Bonds
		Gly A:398 - Arg A:399	[ RasMol ]
		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 ]

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	4h04
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(no "Related Entries Specified in the PDB File" available for 4H04)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (10, 10)

SS Bonds (2, 2)

Cis Peptide Bonds (11, 11)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (9, 9)

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