3GXR - 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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF G-TYPE LYSOZYME FROM ATLANTIC COD (GADUS MORHUA L.) IN COMPLEX WITH NAG OLIGOMERS SHEDS NEW LIGHT ON SUBSTRATE BINDING AND THE CATALYTIC MECHANISM. STRUCTURE WITH NAG TO 1.7

Authors :   R. Helland, R. L. Larsen, S. Finstad, P. Kyomuhendo, A. N. Larsen

Date :   02 Apr 09 (Deposition) - 20 Oct 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Atlantic Cod, Fish Lysozyme, Active Site Residues, Substrate Binding Sites, Surface Potential, Muramidase Activity, Immune System, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Helland, R. L. Larsen, S. Finstad, P. Kyomuhendo, A. N. Larsen
Crystal Structures Of G-Type Lysozyme From Atlantic Cod She New Light On Substrate Binding And The Catalytic Mechanism.
Cell. Mol. Life Sci. V. 66 2585 2009
PubMed-ID: 19543850 | Reference-DOI: 10.1007/S00018-009-0063-X

Molecule 1 - GOOSE-TYPE LYSOZYME 1
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET151/D-TOPO GLYS
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 31-217
	Gene	:	LYSOZYME
	Organism Common	:	ATLANTIC COD
	Organism Scientific	:	GADUS MORHUA
	Organism Taxid	:	8049

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 13)

No.	Name	Count	Type	Full Name
1	NAG	13	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (1, 3)

No.	Name	Count	Type	Full Name
1	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	NAG	-1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 4 (1, 5)

No.	Name	Count	Type	Full Name
1	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:105 , PHE A:127 , THR A:153 , GLY A:154 , ASP A:155 , GLY A:156 , ARG A:157 , NAG A:202	BINDING SITE FOR RESIDUE NAG A 201
02	AC2	SOFTWARE	GLN A:99 , ASP A:101 , TYR A:104 , HIS A:105 , PHE A:127 , TYR A:151 , THR A:153 , ARG A:157 , NAG A:201	BINDING SITE FOR RESIDUE NAG A 202
03	AC3	SOFTWARE	ARG A:72 , GLU A:73 , ILE A:80 , GLY A:89 , ASP A:90 , GLN A:99 , ASN A:152 , THR A:169 , HOH A:207 , HOH A:213 , HOH A:255 , NAG A:302	BINDING SITE FOR RESIDUE NAG A 301
04	AC4	SOFTWARE	GLN A:23 , ARG A:72 , GLU A:73 , HOH A:213 , HOH A:260 , HOH A:266 , NAG A:301 , NAG A:303	BINDING SITE FOR RESIDUE NAG A 302
05	AC5	SOFTWARE	ASP A:24 , ARG A:75 , ASN A:78 , VAL A:79 , HOH A:260 , NAG A:302	BINDING SITE FOR RESIDUE NAG A 303
06	AC6	SOFTWARE	ARG B:72 , GLU B:73 , VAL B:79 , ILE B:80 , GLY B:89 , ASP B:90 , GLN B:99 , ASN B:152 , THR B:169 , NAG B:302	BINDING SITE FOR RESIDUE NAG B 301
07	AC7	SOFTWARE	GLN B:23 , ARG B:72 , GLU B:73 , HOH B:220 , NAG B:301 , NAG B:303 , PRO D:136	BINDING SITE FOR RESIDUE NAG B 302
08	AC8	SOFTWARE	GLN B:23 , ASP B:24 , ARG B:75 , ASN B:78 , VAL B:79 , HOH B:213 , NAG B:302	BINDING SITE FOR RESIDUE NAG B 303
09	AC9	SOFTWARE	HIS D:105 , THR D:153 , GLY D:154 , ASP D:155 , GLY D:156 , ARG D:157 , NAG D:202 , HOH D:223	BINDING SITE FOR RESIDUE NAG D 201
10	BC1	SOFTWARE	ASP D:101 , HIS D:105 , PHE D:127 , TYR D:151 , ASN D:152 , THR D:153 , ARG D:157 , NAG D:201	BINDING SITE FOR RESIDUE NAG D 202
11	BC2	SOFTWARE	ARG D:72 , GLU D:73 , VAL D:79 , ILE D:80 , GLY D:89 , ASP D:90 , GLN D:99 , THR D:169 , HOH D:236 , NAG D:302	BINDING SITE FOR RESIDUE NAG D 301
12	BC3	SOFTWARE	GLN D:23 , ARG D:72 , GLU D:73 , ARG D:75 , NAG D:301 , NAG D:303	BINDING SITE FOR RESIDUE NAG D 302
13	BC4	SOFTWARE	GLN D:23 , ASP D:24 , ARG D:75 , ASN D:78 , VAL D:79 , NAG D:302	BINDING SITE FOR RESIDUE NAG D 303

(no "SS Bond" information available for 3GXR)

Asymmetric Unit

No.	Residues
1	Thr A:84	-	Pro A:85
2	Asn A:91	-	Tyr A:92
3	Thr B:84	-	Pro B:85
4	Gly C:4	-	Tyr C:5
5	Tyr C:5	-	Gly C:6
6	Gly D:4	-	Tyr D:5
7	Tyr D:5	-	Gly D:6
8	Thr D:84	-	Pro D:85

(no "SAP(SNP)/Variant" information available for 3GXR)

(no "PROSITE Motif" information available for 3GXR)

(no "Exon" information available for 3GXR)

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:185
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:185
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
         B9TU22_GADMO    33 YGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxra_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains 3gxrA00 A:5-189  [code=1.10.530.10, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh............ee....ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxr A   5 YGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:183
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
         B9TU22_GADMO    35 DITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxrb_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3gxrB00 B:7-189  [code=1.10.530.10, no name defined]                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh............ee....ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxr B   7 DITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186

Chain C from PDB  Type:PROTEIN  Length:174
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:187
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         B9TU22_GADMO    31 VGYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxrc_ C: automated matches                                                                                                                                                                SCOP domains
               CATH domains 3gxrC00 C:3-189  [code=1.10.530.10, no name defined]                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh-------------..ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxr C   3 VGYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGN-------------YNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    12        22        32        42        52        62        72     |   -        92       102       112       122       132       142       152       162       172       182       
                                                                                                      78            92

Chain D from PDB  Type:PROTEIN  Length:186
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:186
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         B9TU22_GADMO    32 GYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxrd_ D: automated matches                                                                                                                                                               SCOP domains
               CATH domains 3gxrD00 D:4-189  [code=1.10.530.10, no name defined]                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.....hhhhhhh.....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh............ee....ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gxr D   4 GYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: G-type lysozyme (8)

Protein domain: automated matches (4)

Atlantic cod (Gadus morhua) [TaxId: 8049] (2)

1a	d3gxra_	A:
1b	d3gxrb_	B:
1c	d3gxrc_	C:
1d	d3gxrd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Atlantic cod (Gadus morhua) (2)

1a	3gxrC00	C:3-189
1b	3gxrB00	B:7-189
1c	3gxrA00	A:5-189
1d	3gxrD00	D:4-189

(no "Pfam Domain" information available for 3GXR)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (B9TU22_GADMO | B9TU22)

molecular function
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
	GO:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	GO:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

Asymmetric Unit
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	Cis Peptide Bonds
		Asn A:91 - Tyr A:92	[ RasMol ]
		Gly C:4 - Tyr C:5	[ RasMol ]
		Gly D:4 - Tyr D:5	[ RasMol ]
		Thr A:84 - Pro A:85	[ RasMol ]
		Thr B:84 - Pro B:85	[ RasMol ]
		Thr D:84 - Pro D:85	[ RasMol ]
		Tyr C:5 - Gly C:6	[ RasMol ]
		Tyr D:5 - Gly D:6	[ RasMol ]

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Access by PDB/NDB ID
	3gxr
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	B9TU22_GADMO \| B9TU22
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	3.2.1.17
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	B9TU22_GADMO \| B9TU22	:	3gxk

3gxk	THE SAME PROTEIN WITHOUT LIGAND

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 13)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (8, 8)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Related Entries

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Related Entries Specified in the PDB File