1MUQ - JenaLib

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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 :   X-RAY CRYSTAL STRUCTURE OF RATTLESNAKE VENOM COMPLEXED WITH THIODIGALACTOSIDE

Authors :   J. R. Walker, B. Nagar, N. M. Young, T. Hirama, J. M. Rini

Date :   24 Sep 02 (Deposition) - 01 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   C-Type Lectin, Protein-Carbohydrate Complex, Decamer, Calcium Binding, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Walker, B. Nagar, N. M. Young, T. Hirama, J. M. Rini
X-Ray Crystal Structure Of A Galactose-Specific C-Type Lectin Possessing A Novel Decameric Quaternary Structure.
Biochemistry V. 43 3783 2004
PubMed-ID: 15049685 | Reference-DOI: 10.1021/BI035871A
(for further references see the PDB file header)

Molecule 1 - GALACTOSE-SPECIFIC LECTIN
	Chains	:	A, B, C, D, E
	Organism Common	:	WESTERN DIAMONDBACK RATTLESNAKE
	Organism Scientific	:	CROTALUS ATROX
	Organism Taxid	:	8730
	Other Details	:	ISOLATED FROM VENOM
	Synonym	:	RSL (RATTLESNAKE LECTIN)

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (2x)	:	A	B	C	D	E
Biological Unit 2 (1x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 14)

No.	Name	Count	Type	Full Name
1	CA	5	Ligand/Ion	CALCIUM ION
2	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
3	NA	5	Ligand/Ion	SODIUM ION
4	TDG	1	Ligand/Ion	THIODIGALACTOSIDE

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GAL	6	Ligand/Ion	BETA-D-GALACTOSE
3	NA	-1	Ligand/Ion	SODIUM ION
4	TDG	2	Ligand/Ion	THIODIGALACTOSIDE

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	GAL	3	Ligand/Ion	BETA-D-GALACTOSE
3	NA	-1	Ligand/Ion	SODIUM ION
4	TDG	1	Ligand/Ion	THIODIGALACTOSIDE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLN A:96 , ASP A:98 , GLU A:104 , ASN A:119 , ASP A:120 , CA A:201 , HOH A:310 , HOH A:319	BINDING SITE FOR RESIDUE GAL A 301
02	AC2	SOFTWARE	GLN C:96 , ASP C:98 , GLU C:104 , ASN C:119 , ASP C:120 , CA C:203 , HOH C:320 , HOH C:322 , HOH C:329	BINDING SITE FOR RESIDUE GAL C 304
03	AC3	SOFTWARE	GLN E:96 , ASP E:98 , TYR E:100 , GLU E:104 , ASN E:119 , ASP E:120 , CA E:205 , HOH E:321	BINDING SITE FOR RESIDUE GAL E 305
04	AC4	SOFTWARE	GLN A:96 , ASP A:98 , GLU A:104 , ASN A:119 , ASP A:120 , GAL A:301	BINDING SITE FOR RESIDUE CA A 201
05	AC5	SOFTWARE	GLN B:96 , ASP B:98 , GLU B:104 , ASN B:119 , ASP B:120 , TDG B:302	BINDING SITE FOR RESIDUE CA B 202
06	AC6	SOFTWARE	GLN C:96 , ASP C:98 , GLU C:104 , ASN C:119 , ASP C:120 , GAL C:304	BINDING SITE FOR RESIDUE CA C 203
07	AC7	SOFTWARE	GLN D:96 , ASP D:98 , GLU D:104 , ASN D:119 , ASP D:120	BINDING SITE FOR RESIDUE CA D 204
08	AC8	SOFTWARE	GLN E:96 , ASP E:98 , GLU E:104 , ASN E:119 , ASP E:120 , GAL E:305	BINDING SITE FOR RESIDUE CA E 205
09	AC9	SOFTWARE	TYR A:15 , SER A:42 , HIS A:44 , GLN A:132 , HOH A:306	BINDING SITE FOR RESIDUE NA A 206
10	BC1	SOFTWARE	TYR B:15 , SER B:42 , GLN B:132	BINDING SITE FOR RESIDUE NA B 207
11	BC2	SOFTWARE	LEU C:13 , TYR C:15 , SER C:42 , GLN C:132 , HOH C:311	BINDING SITE FOR RESIDUE NA C 208
12	BC3	SOFTWARE	LEU D:13 , TYR D:15 , SER D:42 , GLN D:132	BINDING SITE FOR RESIDUE NA D 209
13	BC4	SOFTWARE	LEU E:13 , TYR E:15 , SER E:42 , GLN E:132 , HOH E:314	BINDING SITE FOR RESIDUE NA E 210
14	BC5	SOFTWARE	GLN B:96 , ASP B:98 , TYR B:100 , GLU B:104 , ASN B:119 , ASP B:120 , CA B:202 , HOH B:312 , TYR C:34 , LYS C:35 , LEU D:5	BINDING SITE FOR RESIDUE TDG B 302

Asymmetric Unit

No.	Residues
1	A:3	-	A:14
2	A:31	-	A:131
3	A:38	-	A:133
4	A:86	-	E:86
5	A:106	-	A:123
6	B:3	-	B:14
7	B:31	-	B:131
8	B:38	-	B:133
9	B:106	-	B:123
10	C:3	-	C:14
11	C:31	-	C:131
12	C:38	-	C:133
13	C:86	-	C:86
14	C:106	-	C:123
15	D:3	-	D:14
16	D:31	-	D:131
17	D:38	-	D:133
18	D:106	-	D:123
19	E:3	-	E:14
20	E:31	-	E:131
21	E:38	-	E:133
22	E:106	-	E:123

Asymmetric Unit

No.	Residues
1	Gln A:96	-	Pro A:97
2	Gln B:96	-	Pro B:97
3	Gln C:96	-	Pro C:97
4	Gln D:96	-	Pro D:97
5	Gln E:96	-	Pro E:97

(no "SAP(SNP)/Variant" information available for 1MUQ)

Asymmetric Unit (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	LECG_CROAT	10-132	5	A:10-132 B:10-132 C:10-132 D:10-132 E:10-132
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	LECG_CROAT	106-131	5	A:106-131 B:106-131 C:106-131 D:106-131 E:106-131

Biological Unit 1 (2, 20)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	LECG_CROAT	10-132	10	A:10-132 B:10-132 C:10-132 D:10-132 E:10-132
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	LECG_CROAT	106-131	10	A:106-131 B:106-131 C:106-131 D:106-131 E:106-131

Biological Unit 2 (2, 10)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	LECG_CROAT	10-132	5	A:10-132 B:10-132 C:10-132 D:10-132 E:10-132
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	LECG_CROAT	106-131	5	A:106-131 B:106-131 C:106-131 D:106-131 E:106-131

(no "Exon" information available for 1MUQ)

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:134
 aligned with LECG_CROAT | P21963 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LECG_CROAT     2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
               SCOP domains d1muqa_ A: Galactose-specific C-type lectin                                                                                            SCOP domains
               CATH domains 1muqA00 A:2-135 Mannose-Binding Protein A, subunit A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhh.....eeeeee........ee.................hhhh.eeeeee.hhhh...eeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:10-132 UniProt: 10-132                                                                             --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1muq A   2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain B from PDB  Type:PROTEIN  Length:134
 aligned with LECG_CROAT | P21963 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LECG_CROAT     2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
               SCOP domains d1muqb_ B: Galactose-specific C-type lectin                                                                                            SCOP domains
               CATH domains 1muqB00 B:2-135 Mannose-Binding Protein A, subunit A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh..eee....hhhhhhhhhhhhhhhh.....eeeeee........ee.................hhhhh..eeee.hhhh...eeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: B:10-132 UniProt: 10-132                                                                             --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1muq B   2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain C from PDB  Type:PROTEIN  Length:134
 aligned with LECG_CROAT | P21963 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LECG_CROAT     2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
               SCOP domains d1muqc_ C: Galactose-specific C-type lectin                                                                                            SCOP domains
               CATH domains 1muqC00 C:2-135 Mannose-Binding Protein A, subunit A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh....eee....hhhhhhhhhhhhhhhh.....eeeeee........ee.................hhhhh..eeee.hhhh...eeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: C:10-132 UniProt: 10-132                                                                             --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1muq C   2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain D from PDB  Type:PROTEIN  Length:134
 aligned with LECG_CROAT | P21963 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LECG_CROAT     2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
               SCOP domains d1muqd_ D: Galactose-specific C-type lectin                                                                                            SCOP domains
               CATH domains 1muqD00 D:2-135 Mannose-Binding Protein A, subunit A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.....eeeeee........ee.................hhhhh..eeee.hhhh...eeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: D:10-132 UniProt: 10-132                                                                             --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1muq D   2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Chain E from PDB  Type:PROTEIN  Length:134
 aligned with LECG_CROAT | P21963 from UniProtKB/Swiss-Prot  Length:135

    Alignment length:134
                                    11        21        31        41        51        61        71        81        91       101       111       121       131    
           LECG_CROAT     2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
               SCOP domains d1muqe_ E: Galactose-specific C-type lectin                                                                                            SCOP domains
               CATH domains 1muqE00 E:2-135 Mannose-Binding Protein A, subunit A                                                                                   CATH domains
           Pfam domains (1) ------------------Lectin_C-1muqE01 E:20-133                                                                                         -- Pfam domains (1)
           Pfam domains (2) ------------------Lectin_C-1muqE02 E:20-133                                                                                         -- Pfam domains (2)
           Pfam domains (3) ------------------Lectin_C-1muqE03 E:20-133                                                                                         -- Pfam domains (3)
           Pfam domains (4) ------------------Lectin_C-1muqE04 E:20-133                                                                                         -- Pfam domains (4)
           Pfam domains (5) ------------------Lectin_C-1muqE05 E:20-133                                                                                         -- Pfam domains (5)
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhhh.....eeeeee........ee.................hhhh.eeeeee.hhhh...eeeee....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: E:10-132 UniProt: 10-132                                                                             --- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1muq E   2 NCPLDWLPMNGLCYKIFNQLKTWEDAEMFCRKYKPGCHLASFHRYGESLEIAEYISDYHKGQENVWIGLRDKKKDFSWEWTDRSCTDYLTWDKNQPDHYQNKEFCVELVSLTGYRLWNDQVCESKDAFLCQCKF 135
                                    11        21        31        41        51        61        71        81        91       101       111       121       131

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: C-type lectin domain (182)

Protein domain: Galactose-specific C-type lectin (2)

Western diamondback rattlesnake (Crotalus atrox) [TaxId: 8730] (2)

1a	d1muqa_	A:
1b	d1muqb_	B:
1c	d1muqc_	C:
1d	d1muqd_	D:
1e	d1muqe_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Mannose-Binding Protein A; Chain A (180)

Homologous Superfamily: Mannose-Binding Protein A, subunit A (180)

Western diamondback rattlesnake (Crotalus atrox) (2)

1a	1muqA00	A:2-135
1b	1muqB00	B:2-135
1c	1muqC00	C:2-135
1d	1muqD00	D:2-135
1e	1muqE00	E:2-135

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: C_Lectin (98)

Family: Lectin_C (85)

Crotalus atrox (Western diamondback rattlesnake) (2)

1a	Lectin_C-1muqE01	E:20-133
1b	Lectin_C-1muqE02	E:20-133
1c	Lectin_C-1muqE03	E:20-133
1d	Lectin_C-1muqE04	E:20-133
1e	Lectin_C-1muqE05	E:20-133

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (LECG_CROAT | P21963)

molecular function
	GO:0030246	carbohydrate binding	Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Asymmetric Unit
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	Cis Peptide Bonds
		Gln A:96 - Pro A:97	[ RasMol ]
		Gln B:96 - Pro B:97	[ RasMol ]
		Gln C:96 - Pro C:97	[ RasMol ]
		Gln D:96 - Pro D:97	[ RasMol ]
		Gln E:96 - Pro E:97	[ RasMol ]

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	1muq
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UniProtKB/Swiss-Prot
	LECG_CROAT \| P21963	:	1jzn

1jzn	X-RAY CRYSTAL STRUCTURE OF RATTLESNAKE VENOM LECTIN COMPLEXED WITH LACTOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 14)

Sites (14, 14)

SS Bonds (22, 22)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 10)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 5)

CATH Domains (1, 5)

Pfam Domains (1, 5)

Gene Ontology (3, 3)

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