2MLL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   MISTLETOE LECTIN I FROM VISCUM ALBUM

Authors :   R. Krauspenhaar, S. Eschenburg, M. Perbandt, V. Kornilov, N. Konareva I. Mikailova, S. Stoeva, R. Wacker, T. Maier, T. P. Singh, A. Mikhailov W. Voelter, C. Betzel

Date :   16 Mar 99 (Deposition) - 20 Mar 00 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Ribosome-Inactivating Protein Type Ii, Ribosome (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Krauspenhaar, S. Eschenburg, M. Perbandt, V. Kornilov, N. Konareva, I. Mikailova, S. Stoeva, R. Wacker, T. Maier, T. Singh, A. Mikhailov, W. Voelter, C. Betzel
Crystal Structure Of Mistletoe Lectin I From Viscum Album.
Biochem. Biophys. Res. Commun. V. 257 418 1999
PubMed-ID: 10198229 | Reference-DOI: 10.1006/BBRC.1999.0470

Molecule 1 - PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)
	Chains	:	A
	Organism Common	:	EUROPEAN MISTLETOE
	Organism Scientific	:	VISCUM ALBUM
	Organism Taxid	:	3972

Molecule 2 - PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)
	Chains	:	B
	Organism Common	:	EUROPEAN MISTLETOE
	Organism Scientific	:	VISCUM ALBUM
	Organism Taxid	:	3972

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 3)

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

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:376 , TRP B:90 , ASN B:92 , LEU B:222 , HOH B:371	BINDING SITE FOR RESIDUE NAG B 301
2	AC2	SOFTWARE	PRO A:212 , THR B:7 , ASN B:40 , ASN B:132 , HOH B:349	BINDING SITE FOR RESIDUE NAG B 302
3	AC3	SOFTWARE	ASN A:108 , ASP A:113	BINDING SITE FOR RESIDUE NAG A 303

Asymmetric/Biological Unit

No.	Residues
1	A:241	-	B:1
2	B:60	-	B:77
3	B:148	-	B:161
4	B:186	-	B:202

(no "Cis Peptide Bond" information available for 2MLL)

Asymmetric/Biological Unit (7, 7)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_ML1_VISAL_013 *	N	319	S	ML1_VISAL	---	---	B	N	14	S
2	UniProt	VAR_ML1_VISAL_014 *	G	357	N	ML1_VISAL	---	---	B	G	52	N
3	UniProt	VAR_ML1_VISAL_015 *	G	458	Q	ML1_VISAL	---	---	B	G	153	Q
4	UniProt	VAR_ML1_VISAL_016 *	C	495	V	ML1_VISAL	---	---	B	S	189	V
5	UniProt	VAR_ML1_VISAL_017 *	G	524	Y	ML1_VISAL	---	---	B	G	217	Y
6	UniProt	VAR_ML1_VISAL_018 *	N	531	S	ML1_VISAL	---	---	B	N	224	S
7	UniProt	VAR_ML1_VISAL_019 *	N	531	T	ML1_VISAL	---	---	B	N	224	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	ML4_VISAL	269-396 400-519	2	B:4-131 B:135-254
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	ML1_VISAL	309-436 440-563	2	B:4-131 B:135-254

(no "Exon" information available for 2MLL)

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:241
 aligned with ML4_VISAL | Q6ITZ3 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:241
                                                                                                                        93                                                                                                                                                   
                                                                                                                      92 |                                                                                                                                                   
                                    10        20        30        40        50        60        70        80        90 | |    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239 
            ML4_VISAL     1 YERLDLDVTSQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSGGGVEAARFVLVELTNEGGDSITAAIDVTNLYVVAYQAGSQSYFLSGPG-THLFTGTTRSSLPFNGSYPDLEQYAGHRKQIPLGIDQLIQSVTALRFPGNTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTEGVFNNPIRLAIPGNFVTLTNVRDVIASLAIMLFVC 240
               SCOP domains d2mlla_ A: Mistletoe lectin I A-chain                                                                                                                                                                                                             SCOP domains
               CATH domains 2mllA01 A:1-162 Ricin (A subunit), domain 1                                                                                                                       2mllA02 A:163-241 Ricin (A Subunit), domain 2                                   CATH domains
               Pfam domains ----RIP-2mllA01 A:5-204                                                                                                                                                                                     ------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhh.......................eeeeeeee....eeeeeee.....eeeee...eeee.............eeee......hhhhhhhh..hhh.....hhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.........eee......eee..hhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mll A   1 YERGDLDVTAQTTGAGYFSFITLLRDYVSSGSFSNAIPLLSQSGGGGEAGRFVLVELTNSGGDGITVAIDVTNLYVVAYQAGSQSYFLSGPGGRGGFTGTTRSSLPFNGSYPDLEQYGGQRKQIPLGIDQLIQSVTALKFPGSTRTGARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIALADPGGGVTLTNVRDVIASLAIMLFVC 241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:259
                                   315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555         
            ML1_VISAL   306 CSASEPTVRIVGRNGMCVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVISQQNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGKPNQMWLPVP 564
               SCOP domains d2mllb1 B:1-133 Plant cytotoxin B-chain (lectin)                                                                                     d2mllb2 B:134-255 Plant cytot oxin B-chain (lectin)                                                                            SCOP domains
               CATH domains 2mllB01 B:1-135  [code=2.80.10.50, no name defined]                                                                                    2mllB02 B:136-255  [code=2. 80.10.50, no name defined]                                                                       CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2mllB01 B:135--251                              -                                   --                    ---- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2mllB02 B:135--251                              -                                   --                    ---- Pfam domains (2)
         Sec.struct. author ............hhh.eeeehhh.......eeee.......hhh...............eeee........eeee......hhhh.eee.....eee.....eee..........eee.....hhh..........eeeeeeehhheeeeee..eeeeee..-......eeee...eeee.................-..........hhh.eee.....eee.....eeee.--.hhh..eeee.....hhh.eeee. Sec.struct. author
             SAPs(SNPs) (1) -------------S-------------------------------------N----------------------------------------------------------------------------------------------------Q------------------------------------V----------------------------Y------S--------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------- SAPs(SNPs) (2)
                PROSITE (2) ---RICIN_B_LECTIN  PDB: B:4-131 UniProt: 309-436                                                                                   ---RICIN_B_LECTIN  PDB: B:135-254 UniProt: 440-563                                                                             - PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mll B   1 CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCATAVGEATVWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESGGGSVTVETCS-SGKADKWALYGDGSIRPEQNQAQCLTSGGDSVAG-VNIVSCSGAASGQRWVFTNEGAILNLKNGLAMDVA--NPGGGRIIIYPATGKPNQMWLPVF 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 | |   169       179       189      |198       208       218       228  |  | 236       246         
                                                                                                                                                                                           162 |                              196 |                               231  |                       
                                                                                                                                                                                             163                                197                                  232

Chain B from PDB  Type:PROTEIN  Length:255
 aligned with ML4_VISAL | Q6ITZ3 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:255
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     
            ML4_VISAL   266 CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLALAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESNGGSVWVETCVSQQNDRWALYGDGSIRPEQNQDQCLTSGRDSVAGINIVSCSGGSSGQRWVFTNEGAILNLKNGLAMDVANPGLGQIIIYPATGKPNQMWLPVP 520
               SCOP domains d2mllb1 B:1-133 Plant cytotoxin B-chain (lectin)                                                                                     d2mllb2 B:134-255 Plant cytotoxin B-chain (lectin)                                                                         SCOP domains
               CATH domains 2mllB01 B:1-135  [code=2.80.10.50, no name defined]                                                                                    2mllB02 B:136-255  [code=2.80.10.50, no name defined]                                                                    CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2mllB01 B:135-251                                                                                     ---- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------Ricin_B_lectin-2mllB02 B:135-251                                                                                     ---- Pfam domains (2)
         Sec.struct. author ............hhh.eeeehhh.......eeee.......hhh...............eeee........eeee......hhhh.eee.....eee.....eee..........eee.....hhh..........eeeeeeehhheeeeee..eeeeee........eeee...eeee...........................hhh.eee.....eee.....eeee..hhh..eeee.....hhh.eeee. Sec.struct. author
             SAPs(SNPs) (1) -------------S-------------------------------------N----------------------------------------------------------------------------------------------------Q-----------------------------------V---------------------------Y------S------------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------------------- SAPs(SNPs) (2)
                    PROSITE ---RICIN_B_LECTIN  PDB: B:4-131 UniProt: 269-396                                                                                   ---RICIN_B_LECTIN  PDB: B:135-254 UniProt: 400-519                                                                         - PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2mll B   1 CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCATAVGEATVWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESGGGSVTVETCSSGKADKWALYGDGSIRPEQNQAQCLTSGGDSVAGVNIVSCSGAASGQRWVFTNEGAILNLKNGLAMDVANPGGGRIIIYPATGKPNQMWLPVF 255
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250

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

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Trefoil (131)

Family: Ricin_B_lectin (25)

Viscum album (European mistletoe) (9)

1a	Ricin_B_lectin-2mllB01	B:135-251
1b	Ricin_B_lectin-2mllB02	B:135-251

Clan: no clan defined [family: RIP] (62)

Family: RIP (62)

Viscum album (European mistletoe) (9)

RIP-2mllA01

A:5-204

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ML4_VISAL | Q6ITZ3)

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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030598	rRNA N-glycosylase activity	Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Chain B (ML1_VISAL | P81446)

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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0030598	rRNA N-glycosylase activity	Catalysis of the hydrolysis of the N-glycosylic bond at A-4324 in 28S rRNA from rat ribosomes or corresponding sites in 28S RNA from other species.
biological process
	GO:0006952	defense response	Reactions, triggered in response to the presence of a foreign body or the occurrence of an injury, which result in restriction of damage to the organism attacked or prevention/recovery from the infection caused by the attack.
	GO:0017148	negative regulation of translation	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Asymmetric/Biological Unit
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(no "Related Entries Specified in the PDB File" available for 2MLL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (7, 7)

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