1ULM - JenaLib

Title :   CRYSTAL STRUCTURE OF POKEWEED LECTIN-D2 COMPLEXED WITH TRI-N-ACETYLCHITOTRIOSE

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

Date :   12 Sep 03 (Deposition) - 23 Dec 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Lectin, Chitin-Binding, Hevein Domain, 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

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:20 , TRP A:22 , TYR A:24 , TYR A:31 , TRP A:43 , CYS A:66 , NAG A:302 , HOH A:312 , HOH A:335	BINDING SITE FOR RESIDUE NAG A 301
2	AC2	SOFTWARE	TRP A:22 , SER A:61 , TRP A:65 , ASP A:71 , HIS A:72 , NAG A:301 , NAG A:303 , HOH A:330 , HOH A:375	BINDING SITE FOR RESIDUE NAG A 302
3	AC3	SOFTWARE	TRP A:22 , GLU A:56 , TYR A:63 , NAG A:302 , HOH A:320 , HOH A:323 , HOH A:343 , SER B:109	BINDING SITE FOR RESIDUE NAG A 303
4	AC4	SOFTWARE	SER B:120 , TYR B:124 , TYR B:131 , TRP B:165 , CYS B:166 , NAG B:402 , HOH B:407 , HOH B:452	BINDING SITE FOR RESIDUE NAG B 401
5	AC5	SOFTWARE	TRP B:122 , SER B:161 , TRP B:165 , ASP B:171 , HIS B:172 , NAG B:401 , NAG B:403	BINDING SITE FOR RESIDUE NAG B 402
6	AC6	SOFTWARE	SER A:9 , TRP B:122 , GLU B:155 , GLU B:156 , TYR B:163 , TYR B:168 , NAG B:402	BINDING SITE FOR RESIDUE NAG B 403

SS Bonds (16, 16)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHIT_BIND_I_2	PS50941	Chitin-binding type-1 domain profile.	LED2_PHYAM	1-42 44-82	4	A:1-42 B:101-142 A:44-82 B:144-182
2	CHIT_BIND_I_1	PS00026	Chitin recognition or binding domain signature.	LED2_PHYAM	13-32	2	A:13-32 B:113-132

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHIT_BIND_I_2	PS50941	Chitin-binding type-1 domain profile.	LED2_PHYAM	1-42 44-82	2	A:1-42 - A:44-82 -
2	CHIT_BIND_I_1	PS00026	Chitin recognition or binding domain signature.	LED2_PHYAM	13-32	1	A:13-32 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CHIT_BIND_I_2	PS50941	Chitin-binding type-1 domain profile.	LED2_PHYAM	1-42 44-82	2	- B:101-142 - B:144-182
2	CHIT_BIND_I_1	PS00026	Chitin recognition or binding domain signature.	LED2_PHYAM	13-32	1	- B:113-132

Exons (0, 0)

Sequences/Alignments

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)
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	(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:82
 aligned with LED2_PHYAM | P83790 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:82
                                    10        20        30        40        50        60        70        80  
           LED2_PHYAM     1 APECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQCD  82
               SCOP domains d1ulma1 A:1-42 Lectin-D                   d1ulma2 A:43-82 Lectin-D                 SCOP domains
               CATH domains 1ulmA01 A:1-40                          1ulmA02 A:41-82                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....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: 1-42  -CHIT_BIND_I_2  PDB: A:44-82             PROSITE (1)
                PROSITE (2) ------------CHIT_BIND_I_1       -------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1ulm A   1 APECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQCD  82
                                    10        20        30        40        50        60        70        80

Chain B from PDB  Type:PROTEIN  Length:82
 aligned with LED2_PHYAM | P83790 from UniProtKB/Swiss-Prot  Length:82

    Alignment length:82
                                    10        20        30        40        50        60        70        80  
           LED2_PHYAM     1 APECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQCD  82
               SCOP domains d1ulmb1 B:101-142 Lectin-D                d1ulmb2 B:143-182 Lectin-D               SCOP domains
               CATH domains 1ulmB01 B:101-140                       1ulmB02 B:141-182                          CATH domains
           Pfam domains (1) ------------------------------------------Chitin_bind_1-1ulmB01 B:143-181        - Pfam domains (1)
           Pfam domains (2) ------------------------------------------Chitin_bind_1-1ulmB02 B:143-181        - Pfam domains (2)
           Pfam domains (3) ------------------------------------------Chitin_bind_1-1ulmB03 B:143-181        - Pfam domains (3)
           Pfam domains (4) ------------------------------------------Chitin_bind_1-1ulmB04 B:143-181        - Pfam domains (4)
         Sec.struct. author ....hhhhh...hhhhhee.....ee.hhhhhh............hhhhh........ee.....ee.hhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CHIT_BIND_I_2  PDB: B:101-142             -CHIT_BIND_I_2  PDB: B:144-182           PROSITE (1)
                PROSITE (2) ------------CHIT_BIND_I_1       -------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------- Transcript
                 1ulm B 101 APECGERASGKRCPNGKCCSQWGYCGTTDNYCGQGCQSQCDYWRCGRDFGGRLCEEDMCCSKYGWCGYSDDHCEDGCQSQCD 182
                                   110       120       130       140       150       160       170       180

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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 '\|'

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (1, 4)

Gene Ontology (4, 4)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LED2_PHYAM | P83790)

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.

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