5ABH - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF GH84 WITH LIGAND

Authors :   M. Bergeron-Brlek, J. Goodwin-Tindall, N. Cekic, V. Varghese, W. F. Za X. Shan, C. Roth, S. Chan, G. J. Davies, D. J. Vocadlo, R. Britton

Date :   05 Aug 15 (Deposition) - 18 Nov 15 (Release) - 27 Jan 16 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.95

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

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

Reference :   M. Bergeron-Brlek, J. Goodwin-Tindall, N. Cekic, C. Roth, W. F. Zandberg, X. Shan, V. Varghese, S. Chan, G. J. Davies, D. J. Vocadlo, R. Britton
A Convenient Approach To Stereoisomeric Iminocyclitols: Generation Of Potent Brain-Permeable Oga Inhibitors.
Angew. Chem. Int. Ed. Engl. V. 54 15429 2015
PubMed-ID: 26545827 | Reference-DOI: 10.1002/ANIE.201507985

Molecule 1 - O-GLCNACASE BT_4395
	Chains	:	A, B
	EC Number	:	3.2.1.169, 3.2.1.52
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	GOLD
	Fragment	:	UNP RESIDUES 22-737
	Organism Scientific	:	BACTEROIDES THETAIOTAOMICRON
	Organism Taxid	:	818
	Synonym	:	BETA-N-ACETYLGLUCOSAMINIDASE, BETA-N-ACETYLHEXOSAMINIDASE, BETA-HEXOSAMINIDASE, HEXOSAMINIDASE B, N-ACETYL-BETA- GLUCOSAMINIDASE, GLYCOSIDE HYDROLASE

		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, 6)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
4	YWN	2	Ligand/Ion	2-[(2R,3S,4R,5R)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-PENTYL-PYRROLIDIN-2-YL]-N-METHYL-ETHANAMIDE

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	YWN	1	Ligand/Ion	2-[(2R,3S,4R,5R)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-PENTYL-PYRROLIDIN-2-YL]-N-METHYL-ETHANAMIDE

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
4	YWN	1	Ligand/Ion	2-[(2R,3S,4R,5R)-5-(HYDROXYMETHYL)-3,4-BIS(OXIDANYL)-1-PENTYL-PYRROLIDIN-2-YL]-N-METHYL-ETHANAMIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:442 , ILE A:443 , PRO A:445 , ALA A:446 , HOH A:2249	BINDING SITE FOR RESIDUE CL A1716
2	AC2	SOFTWARE	GLU B:32 , GLU B:61 , ASP B:64 , HOH B:2020 , HOH B:2021 , HOH B:2034	BINDING SITE FOR RESIDUE CA B1716
3	AC3	SOFTWARE	GLY A:135 , PHE A:136 , TYR A:137 , LYS A:166 , ASP A:242 , ASP A:243 , TYR A:282 , TRP A:286 , THR A:310 , VAL A:314 , TRP A:337 , ASN A:339 , VAL A:342 , ASP A:344 , TYR A:345 , ASN A:372 , HOH A:2239	BINDING SITE FOR RESIDUE YWN A1717
4	AC4	SOFTWARE	GLY B:135 , PHE B:136 , TYR B:137 , LYS B:166 , ASP B:242 , ASP B:243 , TYR B:282 , TRP B:286 , THR B:310 , TRP B:337 , ASN B:339 , VAL B:342 , ASP B:344 , TYR B:345 , ASN B:372 , HOH B:2247	BINDING SITE FOR RESIDUE YWN B1717
5	AC5	SOFTWARE	ARG A:347 , GLU A:375 , HIS A:376 , ASN A:546 , ASN A:548 , HOH A:2186 , HOH A:2192	BINDING SITE FOR RESIDUE EDO A1718
6	AC6	SOFTWARE	ARG B:347 , GLU B:375 , HIS B:376 , TRP B:498 , ASN B:546 , ASN B:548 , HOH B:2198 , HOH B:2204	BINDING SITE FOR RESIDUE EDO B1718

(no "SS Bond" information available for 5ABH)

Asymmetric Unit

No.	Residues
1	Gln A:6	-	Pro A:7
2	Ala A:173	-	Pro A:174
3	Phe A:340	-	Pro A:341
4	Gln B:6	-	Pro B:7
5	Ala B:173	-	Pro B:174
6	Phe B:340	-	Pro B:341

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

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

(no "Exon" information available for 5ABH)

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:677
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeee...eeeee.....hhhhhhhhhhhh...ee....eeeeeee..hhhhhhhh.........eeeee....eeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee..........hhhhh..hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh...............hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh............eee.......eeee..eeee......eeeeeeeeeeeeee..........eeee......ee....ee....eeeeeee..eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5abh A   4 SLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFKEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMISNVKNLPLQVKANRVLISPANEVEIELDAIYPGENIQINFGKDAPGRLEISTDGKEWKTVDLSAGLQKAPVKFVRFTFVLTIEK 715
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593     ||606       616    || 635       645       658       668    || 685       695|      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             599|               621|                   653|             673|           695|      
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              603                631                    657              681            709

Chain B from PDB  Type:PROTEIN  Length:669
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeee...eeeee.....hhhhhhhhhhhh..ee.....eeeeeee..hhhhhhhh.........eeeee...eeeeee.hhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeee.......hhhhhhhhhhhhhhh...eeee.................hhhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhh.........eeee....hhhhh....hhhhhhhhhh....eeee.........hhhhhhhhhhhhh..eeeee.......................hhh.eeeeee........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh..................hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhh................eeee..eeee....eeeeeeeeeeeeee..ee.....ee..........eeeeeeeeeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5abh B   2 NVSLQPPPQQLIVQNKTIDLPAVYQLNGGEEANPHAVKVLKELLSGKQSSKKGMLISIGEKGDKSVRKYSRQIPDHKEGYYLSVNEKEIVLAGNDERGTYYALQTFAQLLKDGKLPEVEIKDYPSVRYRGVVEGFYGTPWSHQARLSQLKFYGKNKMNTYIYGPKDDPYHSAPNWRLPYPDKEAAQLQELVAVANENEVDFVWAIHPGQDIKWNKEDRDLLLAKFEKMYQLGVRSFAVFFDDISGEGTNPQKQAELLNYIDEKFAQVKPDINQLVMCPTEYNKSWSNPNGNYLTTLGDKLNPSIQIMWTGDRVISDITRDGISWINERIKRPAYIWWNFPVSDYVRDHLLLGPVYGNDTTIAKEMSGFVTNPMEHAESSKIAIYSVASYAWNPAKYDTWQTWKDAIRTILPSAAEELECFAMHNSDLGPNGHGYRREESMDIQPAAERFLKAFEGKNYDKADFETLQYTFERMKESADILLMNTENKPLIVEITPWVHQFKLTAEMGEEVLKMVEGRNESYFLRKYNHVKALQQQMFYIDQTSNQNPYQPGVKTATRVIKPLIDRTFATVVKFFNQKFNAHLDATTDYMPHKMLPLQVKANRVLISPVEIELDAIYPGENIQINEISTDGKEWKTVDLKQKESRLSAGLQKAPVKFVRFLRQFVLTIEK 715
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451  ||   462       472       482       492       502       512       522       532       542       552       562       572       582       592  ||   611      |633       643   ||  665       675       685       706         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              454|                                                                                                                                        595|          618|             647|                               694|         
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               456                                                                                                                                         605           631              660                                706

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 5ABH)

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

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

Asymmetric Unit(hide GO term definitions)

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:173 - Pro A:174	[ RasMol ]
		Ala B:173 - Pro B:174	[ RasMol ]
		Gln A:6 - Pro A:7	[ RasMol ]
		Gln B:6 - Pro B:7	[ RasMol ]
		Phe A:340 - Pro A:341	[ RasMol ]
		Phe B:340 - Pro B:341	[ RasMol ]

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5abe	STRUCTURE OF GH84 WITH LIGAND
5abf	STRUCTURE OF GH84 WITH LIGAND
5abg	STRUCTURE OF GH84 WITH LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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Gene Ontology (7, 7)

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Related Entries

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Related Entries Specified in the PDB File