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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF POKEWEED LECTIN-C

Authors :   M. Hayashida, T. Fujii, M. Ishiguro, Y. Hata

Date :   12 Sep 03 (Deposition) - 23 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A,B

Keywords :   Lectin, Chitin-Binding Protein, Hevein Domain, Pl-C, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Hayashida, T. Fujii, M. Hamasu, M. Ishiguro, Y. Hata
Similarity Between Protein-Protein And Protein-Carbohydrate Interactions, Revealed By Two Crystal Structures Of Lectins From The Roots Of Pokeweed.
J. Mol. Biol. V. 334 551 2003
PubMed-ID: 14623194 | Reference-DOI: 10.1016/J.JMB.2003.09.076
(for further references see the PDB file header)

Molecule 1 - LECTIN-C
	Chains	:	A, B
	Organism Common	:	AMERICAN POKEWEED
	Organism Scientific	:	PHYTOLACCA AMERICANA
	Organism Taxid	:	3527
	Tissue	:	ROOTS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ULK)

(no "Site" information available for 1ULK)

Asymmetric/Biological Unit

No.	Residues
1	A:4	-	A:19
2	A:13	-	A:25
3	A:18	-	A:32
4	A:36	-	A:40
5	A:45	-	A:60
6	A:54	-	A:66
7	A:59	-	A:73
8	A:77	-	A:81
9	A:86	-	A:101
10	A:95	-	A:107
11	A:100	-	A:114
12	A:118	-	A:122
13	B:204	-	B:219
14	B:213	-	B:225
15	B:218	-	B:232
16	B:236	-	B:240
17	B:245	-	B:260
18	B:254	-	B:266
19	B:259	-	B:273
20	B:277	-	B:281
21	B:286	-	B:301
22	B:295	-	B:307
23	B:300	-	B:314
24	B:318	-	B:322

(no "Cis Peptide Bond" information available for 1ULK)

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

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHIT_BIND_I_2	PS50941	Chitin-binding type-1 domain profile.	LECC_PHYAM	45-86 88-127 129-168	6	A:1-42 B:201-242 A:44-83 B:244-283 A:85-124 B:285-324
2	CHIT_BIND_I_1	PS00026	Chitin recognition or binding domain signature.	LECC_PHYAM	57-76	2	A:13-32 B:213-232

(no "Exon" information available for 1ULK)

Asymmetric/Biological 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:126
 aligned with LECC_PHYAM | Q9AYP9 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:126
                                    54        64        74        84        94       104       114       124       134       144       154       164      
           LECC_PHYAM    45 APVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQCDLPT 170
               SCOP domains d1ulka1 A:1-42 Lectin-C                   d1ulka2 A:43-83 Lectin-C                 d1ulka3 A:84-126 Lectin-C                   SCOP domains
               CATH domains 1ulkA01 A:1-40                          1ulkA02 A:41-81                          1ulkA03 A:82-126                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhh...hhhhhee.....ee.hhhhhh............hhhhh...hhhhhee.....ee.hhhhhh............hhhhh........ee.....ee.hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: A:1-42 UniProt: 45-86 -CHIT_BIND_I_2  PDB: A:44-83             -CHIT_BIND_I_2  PDB: A:85-124            -- PROSITE (1)
                PROSITE (2) ------------CHIT_BIND_I_1       ---------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ulk A   1 APVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQCDLPT 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with LECC_PHYAM | Q9AYP9 from UniProtKB/Swiss-Prot  Length:194

    Alignment length:126
                                    54        64        74        84        94       104       114       124       134       144       154       164      
           LECC_PHYAM    45 APVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQCDLPT 170
               SCOP domains d1ulkb1 B:201-242 Lectin-C                d1ulkb2 B:243-283 Lectin-C               d1ulkb3 B:284-326 Lectin-C                  SCOP domains
               CATH domains 1ulkB01 B:201-240                       1ulkB02 B:241-281                        1ulkB03 B:282-326                             CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------Chitin_bind_1-1ulkB01 B:284-322        ---- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------Chitin_bind_1-1ulkB02 B:284-322        ---- Pfam domains (2)
           Pfam domains (3) -----------------------------------------------------------------------------------Chitin_bind_1-1ulkB03 B:284-322        ---- Pfam domains (3)
           Pfam domains (4) -----------------------------------------------------------------------------------Chitin_bind_1-1ulkB04 B:284-322        ---- Pfam domains (4)
           Pfam domains (5) -----------------------------------------------------------------------------------Chitin_bind_1-1ulkB05 B:284-322        ---- Pfam domains (5)
           Pfam domains (6) -----------------------------------------------------------------------------------Chitin_bind_1-1ulkB06 B:284-322        ---- Pfam domains (6)
         Sec.struct. author ....hhhhh...hhhhhee.....ee.hhhhhh............hhhhh...hhhhhee.....ee...................hhhhh........ee.....ee.hhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: B:201-242             -CHIT_BIND_I_2  PDB: B:244-283           -CHIT_BIND_I_2  PDB: B:285-324           -- PROSITE (1)
                PROSITE (2) ------------CHIT_BIND_I_1       ---------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1ulk B 201 APVCGVRASGRVCPDGYCCSQWGYCGTTEEYCGKGCQSQCDYNRCGKEFGGKECHDELCCSQYGWCGNSDGHCGEGCQSQCSYWRCGKDFGGRLCTEDMCCSQYGWCGLTDDHCEDGCQSQCDLPT 326
                                   210       220       230       240       250       260       270       280       290       300       310       320

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Knottins (small inhibitors, toxins, lectins) (761)

Superfamily: Plant lectins/antimicrobial peptides (31)

Family: Hevein-like agglutinin (lectin) domain (28)

Protein domain: Lectin-C (1)

American pokeweed (Phytolacca americana) [TaxId: 3527] (1)

1a	d1ulka1	A:1-42
1b	d1ulka2	A:43-83
1c	d1ulka3	A:84-126
1d	d1ulkb1	B:201-242
1e	d1ulkb2	B:243-283
1f	d1ulkb3	B:284-326

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Wheat Germ Agglutinin (Isolectin 2); domain 1 (140)

Homologous Superfamily: [code=3.30.60.10, no name defined] (23)

American pokeweed (Phytolacca americana) (4)

1a	1ulkA02	A:41-81
1b	1ulkA01	A:1-40
1c	1ulkB01	B:201-240
1d	1ulkB02	B:241-281
1e	1ulkA03	A:82-126
1f	1ulkB03	B:282-326

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Chitin_bind_1] (17)

Family: Chitin_bind_1 (17)

Phytolacca americana (American pokeweed) (Phytolacca decandra) (4)

1a	Chitin_bind_1-1ulkB01	B:284-322
1b	Chitin_bind_1-1ulkB02	B:284-322
1c	Chitin_bind_1-1ulkB03	B:284-322
1d	Chitin_bind_1-1ulkB04	B:284-322
1e	Chitin_bind_1-1ulkB05	B:284-322
1f	Chitin_bind_1-1ulkB06	B:284-322

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LECC_PHYAM | Q9AYP9)

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:0008061	chitin binding	Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
biological process
	GO:0051781	positive regulation of cell division	Any process that activates or increases the frequency, rate or extent of cell division.
	GO:0045840	positive regulation of mitotic nuclear division	Any process that activates or increases the frequency, rate or extent of mitosis.

Asymmetric/Biological Unit
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1ulm	POKEWEED LECTIN-D2 COMPLEXED WITH TRI-N-ACETYLCHITOTRIOSE

Description

Compounds

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Ligands, Modified Residues, Ions (0, 0)

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SS Bonds (24, 24)

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SCOP Domains (1, 6)

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