2Z48 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF HEMOLYTIC LECTIN CEL-III COMPLEXED WITH GALNAC

Authors :   T. Hatakeyama, H. Unno, S. Eto, H. Hidemura, T. Uchida, Y. Kouzuma

Date :   13 Jun 07 (Deposition) - 30 Oct 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Lectin, Cel-Iii, Hemolysis, Hemagglutination, Pore-Forming, Calcium, Magnesium, Galnac, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Hatakeyama, H. Unno, Y. Kouzuma, T. Uchida, S. Eto, H. Hidemura, N. Kato, M. Yonekura, M. Kusunoki
C-Type Lectin-Like Carbohydrate-Recognition Of The Hemolytic Lectin Cel-Iii Containing Ricin-Type Beta-Trefoil Folds
J. Biol. Chem. V. 282 37826 2007
PubMed-ID: 17977832 | Reference-DOI: 10.1074/JBC.M705604200
(for further references see the PDB file header)

Molecule 1 - HEMOLYTIC LECTIN CEL-III
	Chains	:	A, B
	Fragment	:	RESIDUES IN DATABASE 11-442
	Organism Scientific	:	CUCUMARIA ECHINATA
	Organism Taxid	:	40245

		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, 26)

No.	Name	Count	Type	Full Name
1	A2G	4	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	CA	10	Ligand/Ion	CALCIUM ION
3	MG	4	Ligand/Ion	MAGNESIUM ION
4	NGA	8	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 1 (2, 6)

No.	Name	Count	Type	Full Name
1	A2G	2	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NGA	4	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 2 (2, 6)

No.	Name	Count	Type	Full Name
1	A2G	2	Ligand/Ion	N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	MG	-1	Ligand/Ion	MAGNESIUM ION
4	NGA	4	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:23 , ILE A:24 , VAL A:25 , GLY A:26 , ASN A:27 , TYR A:36 , ASP A:39 , LEU A:41 , GLN A:300 , ARG A:378 , ASN A:410 , CA A:1007 , HOH A:1218	BINDING SITE FOR RESIDUE A2G A 1001
02	AC2	SOFTWARE	ASP A:121 , ILE A:122 , GLU A:123 , GLY A:124 , SER A:125 , TYR A:134 , GLN A:137 , CA A:1102 , HOH A:1269 , HOH A:1379	BINDING SITE FOR RESIDUE NGA A 1002
03	AC3	SOFTWARE	ASP A:168 , VAL A:169 , GLU A:170 , GLY A:171 , SER A:172 , TYR A:181 , GLU A:184 , CA A:1103 , HOH A:1225 , HOH A:1474	BINDING SITE FOR RESIDUE NGA A 1003
04	AC4	SOFTWARE	ASP A:209 , VAL A:210 , GLU A:211 , GLY A:212 , SER A:213 , TYR A:222 , ASP A:225 , CA A:1104 , HOH A:1236 , HOH A:1240 , HOH A:1344 , HOH A:1393 , HOH A:1481 , HOH A:1544 , HOH A:1584 , HOH A:1596	BINDING SITE FOR RESIDUE NGA A 1004
05	AC5	SOFTWARE	ASP A:256 , VAL A:257 , SER A:258 , GLY A:259 , ASP A:260 , TRP A:269 , ASP A:272 , CA A:1205 , HOH A:1213 , HOH A:1289	BINDING SITE FOR RESIDUE A2G A 1005
06	AC6	SOFTWARE	ASP A:9 , GLN A:92 , VAL A:107 , TYR A:145 , VAL A:146 , HOH A:1206 , HOH A:1219 , HOH A:1252 , HOH A:1339 , HOH A:1462 , HOH A:1478 , ASN B:236	BINDING SITE FOR RESIDUE NGA A 1006
07	AC7	SOFTWARE	ASP B:23 , ILE B:24 , VAL B:25 , GLY B:26 , ASN B:27 , TYR B:36 , ASP B:39 , LEU B:41 , GLN B:300 , ARG B:378 , ASN B:410 , CA B:1201 , HOH B:2027 , HOH B:2126 , HOH B:2361	BINDING SITE FOR RESIDUE A2G B 2001
08	AC8	SOFTWARE	ASP B:121 , ILE B:122 , GLU B:123 , GLY B:124 , SER B:125 , TYR B:134 , GLN B:137 , CA B:1202 , HOH B:2064 , HOH B:2145	BINDING SITE FOR RESIDUE NGA B 2002
09	AC9	SOFTWARE	PRO A:77 , ASP B:168 , VAL B:169 , GLU B:170 , GLY B:171 , SER B:172 , TYR B:181 , GLU B:184 , CA B:1203 , HOH B:2053 , HOH B:2187	BINDING SITE FOR RESIDUE NGA B 2003
10	BC1	SOFTWARE	ASP B:209 , VAL B:210 , GLU B:211 , GLY B:212 , SER B:213 , TYR B:222 , ASP B:225 , CA B:1204 , HOH B:2092 , HOH B:2163 , HOH B:2173	BINDING SITE FOR RESIDUE NGA B 2004
11	BC2	SOFTWARE	ASP B:256 , VAL B:257 , SER B:258 , GLY B:259 , ASP B:260 , TRP B:269 , ASP B:272 , CA B:1205 , HOH B:2011 , HOH B:2107 , HOH B:2181 , HOH B:2277	BINDING SITE FOR RESIDUE A2G B 2005
12	BC3	SOFTWARE	ASN A:236 , ASP B:9 , GLN B:92 , VAL B:107 , TYR B:145 , VAL B:146 , HOH B:2018 , HOH B:2037 , HOH B:2115 , HOH B:2156 , HOH B:2198 , HOH B:2237	BINDING SITE FOR RESIDUE NGA B 2006
13	BC4	SOFTWARE	ASP A:23 , ILE A:24 , GLY A:26 , ASP A:43 , A2G A:1001 , HOH A:1218	BINDING SITE FOR RESIDUE CA A 1007
14	BC5	SOFTWARE	ASP A:121 , ILE A:122 , GLY A:124 , ASP A:141 , NGA A:1002 , HOH A:1269	BINDING SITE FOR RESIDUE CA A 1102
15	BC6	SOFTWARE	ASP A:168 , VAL A:169 , GLY A:171 , ASP A:188 , NGA A:1003 , HOH A:1225	BINDING SITE FOR RESIDUE CA A 1103
16	BC7	SOFTWARE	ASP A:209 , VAL A:210 , GLY A:212 , ASP A:229 , NGA A:1004 , HOH A:1236	BINDING SITE FOR RESIDUE CA A 1104
17	BC8	SOFTWARE	ASP A:256 , VAL A:257 , GLY A:259 , ASP A:276 , A2G A:1005 , HOH A:1213	BINDING SITE FOR RESIDUE CA A 1205
18	BC9	SOFTWARE	ASN A:32 , ILE A:33 , ASN A:72 , VAL A:73 , ILE A:131 , HOH A:1273	BINDING SITE FOR RESIDUE MG A 1111
19	CC1	SOFTWARE	ASN A:177 , VAL A:178 , ASN A:218 , VAL A:219 , ASP A:265 , VAL A:266	BINDING SITE FOR RESIDUE MG A 1112
20	CC2	SOFTWARE	ASP B:23 , ILE B:24 , GLY B:26 , ASP B:43 , A2G B:2001 , HOH B:2027	BINDING SITE FOR RESIDUE CA B 1201
21	CC3	SOFTWARE	ASP B:121 , ILE B:122 , GLY B:124 , ASP B:141 , NGA B:2002 , HOH B:2064	BINDING SITE FOR RESIDUE CA B 1202
22	CC4	SOFTWARE	ASP B:168 , VAL B:169 , GLY B:171 , ASP B:188 , NGA B:2003 , HOH B:2053	BINDING SITE FOR RESIDUE CA B 1203
23	CC5	SOFTWARE	ASP B:209 , VAL B:210 , GLY B:212 , ASP B:229 , NGA B:2004 , HOH B:2033	BINDING SITE FOR RESIDUE CA B 1204
24	CC6	SOFTWARE	ASP B:256 , VAL B:257 , GLY B:259 , ASP B:276 , A2G B:2005 , HOH B:2011	BINDING SITE FOR RESIDUE CA B 1205
25	CC7	SOFTWARE	ASN B:32 , ILE B:33 , ASN B:72 , VAL B:73 , ILE B:131 , HOH B:2286	BINDING SITE FOR RESIDUE MG B 1211
26	CC8	SOFTWARE	ASN B:177 , VAL B:178 , ASN B:218 , VAL B:219 , ASP B:265 , VAL B:266	BINDING SITE FOR RESIDUE MG B 1212

Asymmetric Unit

No.	Residues
1	A:4	-	A:49
2	A:21	-	A:38
3	A:62	-	A:78
4	A:119	-	A:136
5	A:166	-	A:183
6	A:207	-	A:224
7	A:239	-	A:244
8	A:254	-	A:271
9	A:298	-	A:380
10	A:367	-	A:406
11	A:415	-	A:429
12	A:421	-	A:426
13	B:4	-	B:49
14	B:21	-	B:38
15	B:62	-	B:78
16	B:119	-	B:136
17	B:166	-	B:183
18	B:207	-	B:224
19	B:239	-	B:244
20	B:254	-	B:271
21	B:298	-	B:380
22	B:367	-	B:406
23	B:415	-	B:429
24	B:421	-	B:426

Asymmetric Unit

No.	Residues
1	Tyr A:81	-	Pro A:82
2	Gly A:359	-	Thr A:360
3	Tyr B:81	-	Pro B:82
4	Gly B:359	-	Thr B:360
5	Thr B:360	-	Thr B:361

(no "SAP(SNP)/Variant" information available for 2Z48)

(no "PROSITE Motif" information available for 2Z48)

(no "Exon" information available for 2Z48)

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:431
 aligned with Q868M7_CUCEC | Q868M7 from UniProtKB/TrEMBL  Length:442

    Alignment length:431
                                    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 
         Q868M7_CUCEC    12 VLCTNPLDIGELRNYKSKQCVDIVGNQGSGNIATHDCDGLSDQQIIMCGDGTIRNEARNYCFTPDGSGNANVMSSPCTLYPEIPSSQRWRLGRKKAFTDNGGIEQVATEIINLASGKCLDVEGSDGTGDIGVYDCQNLDDQYFYIRSRGPELFYGRLRNEKSDLCLDVEGSEGKGNVLMYSCEDNLDQWFRYYENGEIVNAKQGMCLDVEGSDGSGNVGIYRCDDLRDQMWSRPNAYCNGDYCSFLNKESNKCLDVSGDQGTGDVGTWQCDGLPDQRFKWVFDDWEVPTATWNMVGCDQNGKVSQQISNTISFSSTVTAGVAVEVSSTIEKGVIFAKASVSVKVTASLSKAWTNSQSGTTAITYTCDNYDSDEEFTRGCMWQLAIETTEVKSGDLLVWNPQIIKCTRSNTAPGCAPFTKCANEDCTFCTDI 442
               SCOP domains d2z48a1 A:2-150 Hemolytic lectin CEL-III, domains 1 and 2                                                                                            d2z48a2 A:151-283 Hemolytic lectin CEL-III, domains 1 and 2                                                                          d2z48a3 A:284-432 Hemolytic lectin CEL-III, C-terminal domain                                                                                         SCOP domains
               CATH domains 2z48A01 A:2-150  [code=2.80.10.50, no name defined]                                                                                                  2z48A02 A:151-284  [code=2.80.10.50, no name defined]                                                                                 2z48A03 A:285-432 hemolytic lectin cel-iii, domain 3                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.eee.....eeee......eeeeee....hhhh.eeee....eee....eeeee.......eeeee.......hhhh.eeeeeeeeee.....eeeeeeeee.....eeee........eeee....hhh.eeee.....eeeeeeeee.....eeee......eeeeee....hhhh.eeee....eee.....eeee........eeee....hhhh.ee.hhhhh.......ee.....eeee........eeee....hhhh.eeee.......eeeeeeeeee.....eeee..eee.....hhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhhhhhhh......eeee............eeeeeeeeeee......eeeee...eeee............ee.......ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z48 A   2 VLCTNPLDIGELRSFKSKQCVDIVGNQGSGNIATYDCDGLSDQQIIICGDGTIRNEARNYCFTPDGSGNANVMSSPCTLYPEIPSSQRWRQGRRKTFTDNGGIEQVATEIINLASGKCLDIEGSDGTGDIGVYDCQNLDDQYFYVRSRGPELFYGRLRNEKSDLCLDVEGSDGKGNVLMYSCEDNLDQWFRYYENGEIVNAKSGMCLDVEGSDGSGNVGIYRCDDLRDQMWSRPNAYCNGDYCSFLNKESNKCLDVSGDQGTGDVGTWQCDGLPDQRFKWVFDDWEVPTATWNMVGCDQNGKVSQQISNTISFSSTVTAGVAVEVSSTIEKGVIFAKATVSVKVTASLSKAWTNSQSGTTAITYTCDNYDSDEEFTRGCMWQLAIETTEVKSGDLLVWNPQIVKCTRSNTAPGCAPFTKCANEDCTFCTDI 432
                                    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

Chain B from PDB  Type:PROTEIN  Length:431
 aligned with Q868M7_CUCEC | Q868M7 from UniProtKB/TrEMBL  Length:442

    Alignment length:431
                                    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 
         Q868M7_CUCEC    12 VLCTNPLDIGELRNYKSKQCVDIVGNQGSGNIATHDCDGLSDQQIIMCGDGTIRNEARNYCFTPDGSGNANVMSSPCTLYPEIPSSQRWRLGRKKAFTDNGGIEQVATEIINLASGKCLDVEGSDGTGDIGVYDCQNLDDQYFYIRSRGPELFYGRLRNEKSDLCLDVEGSEGKGNVLMYSCEDNLDQWFRYYENGEIVNAKQGMCLDVEGSDGSGNVGIYRCDDLRDQMWSRPNAYCNGDYCSFLNKESNKCLDVSGDQGTGDVGTWQCDGLPDQRFKWVFDDWEVPTATWNMVGCDQNGKVSQQISNTISFSSTVTAGVAVEVSSTIEKGVIFAKASVSVKVTASLSKAWTNSQSGTTAITYTCDNYDSDEEFTRGCMWQLAIETTEVKSGDLLVWNPQIIKCTRSNTAPGCAPFTKCANEDCTFCTDI 442
               SCOP domains d2z48b1 B:2-150 Hemolytic lectin CEL-III, domains 1 and 2                                                                                            d2z48b2 B:151-283 Hemolytic lectin CEL-III, domains 1 and 2                                                                          d2z48b3 B:284-432 Hemolytic lectin CEL-III, C-terminal domain                                                                                         SCOP domains
               CATH domains 2z48B01 B:2-150  [code=2.80.10.50, no name defined]                                                                                                  2z48B02 B:151-284  [code=2.80.10.50, no name defined]                                                                                 2z48B03 B:285-432 hemolytic lectin cel-iii, domain 3                                                                                                 CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.....eeee......eeeeee....hhh.eeeee....eee....eeeee.......eeeee.......hhhh.eeeeeeeeee.....eeeeeeeee.....eeee........eeee....hhhh.eee.....eeeeeeeee.....eeee......eeeeee....hhhh.eeee....eee.....eeee........eeee....hhhh.ee.hhhhh.......ee.....eeee........eeee....hhhh.eeee.......eeeeeeeeee.....eeee..eee.....hhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhhhhhh.......eeee............eeeeeeeeeee......eeeee...eeee............ee.......ee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2z48 B   2 VLCTNPLDIGELRSFKSKQCVDIVGNQGSGNIATYDCDGLSDQQIIICGDGTIRNEARNYCFTPDGSGNANVMSSPCTLYPEIPSSQRWRQGRRKTFTDNGGIEQVATEIINLASGKCLDIEGSDGTGDIGVYDCQNLDDQYFYVRSRGPELFYGRLRNEKSDLCLDVEGSDGKGNVLMYSCEDNLDQWFRYYENGEIVNAKSGMCLDVEGSDGSGNVGIYRCDDLRDQMWSRPNAYCNGDYCSFLNKESNKCLDVSGDQGTGDVGTWQCDGLPDQRFKWVFDDWEVPTATWNMVGCDQNGKVSQQISNTISFSSTVTAGVAVEVSSTIEKGVIFAKATVSVKVTASLSKAWTNSQSGTTAITYTCDNYDSDEEFTRGCMWQLAIETTEVKSGDLLVWNPQIVKCTRSNTAPGCAPFTKCANEDCTFCTDI 432
                                    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

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: hemolytic lectin cel-iii, domain 3 (3)

Homologous Superfamily: hemolytic lectin cel-iii, domain 3 (3)

Cucumaria echinata. Organism_taxid: 40245 (3)

1a	2z48A03	A:285-432
1b	2z48B03	B:285-432

Class: Mainly Beta (13760)

Architecture: Trefoil (289)

Topology: Trefoil (Acidic Fibroblast Growth Factor, subunit A) (289)

Homologous Superfamily: [code=2.80.10.50, no name defined] (289)

Cucumaria echinata. Organism_taxid: 40245 (3)

2a	2z48A01	A:2-150
2b	2z48B01	B:2-150
2c	2z48A02	A:151-284
2d	2z48B02	B:151-284

(no "Pfam Domain" information available for 2Z48)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q868M7_CUCEC | Q868M7)

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly A:359 - Thr A:360	[ RasMol ]
		Gly B:359 - Thr B:360	[ RasMol ]
		Thr B:360 - Thr B:361	[ RasMol ]
		Tyr A:81 - Pro A:82	[ RasMol ]
		Tyr B:81 - Pro B:82	[ RasMol ]

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	2z48
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		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/TrEMBL
	Q868M7_CUCEC \| Q868M7	:	1vcl 2z49 3w9t

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 26)

Sites (26, 26)

SS Bonds (24, 24)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 6)

CATH Domains (2, 6)

Pfam Domains (0, 0)

Gene Ontology (2, 2)

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