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(-) Description

Title :  MISTLETOE LECTIN I FROM VISCUM ALBUM COMPLEXED WITH GALACTOSE
 
Authors :  H. Niwa, A. G. Tonevitsky, I. I. Agapov, S. Saward, U. Pfuller, R. A. Palm
Date :  10 Mar 03  (Deposition) - 01 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Type-Ii Ribosome-Inactivating Protein, Ricin-Like, Beta-Trefoil, Hydrolase-Sugar Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Niwa, A. G. Tonevitsky, I. I. Agapov, S. Saward, U. Pfuller, R. A. Palmer
Crystal Structure At 3 A Of Mistletoe Lectin I, A Dimeric Type-Ii Ribosome-Inactivating Protein, Complexed With Galactose
Eur. J. Biochem. V. 270 2739 2003
PubMed-ID: 12823544  |  Reference-DOI: 10.1046/J.1432-1033.2003.03646.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MISTLETOE LECTIN I
    Chains: A
    EC Number: 3.2.2.22
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Synonym: MLI A-CHAIN, N-GLYCOSIDASE
 
Molecule 2 - MISTLETOE LECTIN I
    Chains: B
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Synonym: MLI B-CHAIN, GALACTOSE-SPECIFIC LECTIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB
Biological Unit 2 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1GAL4Ligand/IonBETA-D-GALACTOSE
2NAG12Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1GAL2Ligand/IonBETA-D-GALACTOSE
2NAG6Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:23 , VAL B:24 , ARG B:25 , ASP B:26 , ASP B:27 , GLN B:36 , TRP B:38 , LYS B:41 , ASN B:47BINDING SITE FOR RESIDUE GAL B 265
2AC2SOFTWAREASP B:235 , GLN B:238 , ASN B:256 , HOH B:402 , HOH B:405BINDING SITE FOR RESIDUE GAL B 267
3AC3SOFTWAREARG A:90 , ASP A:91 , ASN A:112 , SER A:114 , ASP A:117BINDING SITE FOR RESIDUE NAG A 270
4AC4SOFTWAREASP B:27 , PHE B:29 , ASN B:61 , HOH B:426BINDING SITE FOR RESIDUE NAG B 280
5AC5SOFTWAREASN B:96 , LEU B:228 , NAG B:291BINDING SITE FOR RESIDUE NAG B 290
6AC6SOFTWARETRP B:94 , NAG B:290BINDING SITE FOR RESIDUE NAG B 291
7AC7SOFTWAREPHE A:214 , PRO A:217 , THR B:11 , ASN B:44 , ASN B:136 , NAG B:301BINDING SITE FOR RESIDUE NAG B 300
8AC8SOFTWARETHR B:11 , NAG B:300BINDING SITE FOR RESIDUE NAG B 301

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:247 -B:5
2B:64 -B:81
3B:152 -B:165
4B:191 -B:208

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (19, 19)

Asymmetric Unit (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_ML1_VISAL_001 *E48DML1_VISAL  ---  ---AD15D
02UniProtVAR_ML1_VISAL_013 *N319SML1_VISAL  ---  ---BN18S
03UniProtVAR_ML1_VISAL_014 *G357NML1_VISAL  ---  ---BG56N
04UniProtVAR_ML1_VISAL_002 *N145TML1_VISAL  ---  ---AN112T
05UniProtVAR_ML1_VISAL_003 *P149TML1_VISAL  ---  ---AP116T
06UniProtVAR_ML1_VISAL_004 *T173SML1_VISAL  ---  ---AT140S
07UniProtVAR_ML1_VISAL_005 *F177YML1_VISAL  ---  ---AF144Y
08UniProtVAR_ML1_VISAL_006 *T184AML1_VISAL  ---  ---AT151A
09UniProtVAR_ML1_VISAL_015 *G458QML1_VISAL  ---  ---BG157Q
10UniProtVAR_ML1_VISAL_007 *Y212DML1_VISAL  ---  ---AY179D
11UniProtVAR_ML1_VISAL_008 *A217EML1_VISAL  ---  ---AA184E
12UniProtVAR_ML1_VISAL_009 *V223MML1_VISAL  ---  ---AV190M
13UniProtVAR_ML1_VISAL_016 *C495VML1_VISAL  ---  ---BC194V
14UniProtVAR_ML1_VISAL_010 *I251FML1_VISAL  ---  ---AI218F
15UniProtVAR_ML1_VISAL_017 *G524YML1_VISAL  ---  ---BG223Y
16UniProtVAR_ML1_VISAL_018 *N531SML1_VISAL  ---  ---BN230S
17UniProtVAR_ML1_VISAL_019 *N531TML1_VISAL  ---  ---BN230T
18UniProtVAR_ML1_VISAL_011 *T264SML1_VISAL  ---  ---AT231S
19UniProtVAR_ML1_VISAL_012 *D268SML1_VISAL  ---  ---AD235S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (19, 38)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_ML1_VISAL_001 *E48DML1_VISAL  ---  ---AD15D
02UniProtVAR_ML1_VISAL_013 *N319SML1_VISAL  ---  ---BN18S
03UniProtVAR_ML1_VISAL_014 *G357NML1_VISAL  ---  ---BG56N
04UniProtVAR_ML1_VISAL_002 *N145TML1_VISAL  ---  ---AN112T
05UniProtVAR_ML1_VISAL_003 *P149TML1_VISAL  ---  ---AP116T
06UniProtVAR_ML1_VISAL_004 *T173SML1_VISAL  ---  ---AT140S
07UniProtVAR_ML1_VISAL_005 *F177YML1_VISAL  ---  ---AF144Y
08UniProtVAR_ML1_VISAL_006 *T184AML1_VISAL  ---  ---AT151A
09UniProtVAR_ML1_VISAL_015 *G458QML1_VISAL  ---  ---BG157Q
10UniProtVAR_ML1_VISAL_007 *Y212DML1_VISAL  ---  ---AY179D
11UniProtVAR_ML1_VISAL_008 *A217EML1_VISAL  ---  ---AA184E
12UniProtVAR_ML1_VISAL_009 *V223MML1_VISAL  ---  ---AV190M
13UniProtVAR_ML1_VISAL_016 *C495VML1_VISAL  ---  ---BC194V
14UniProtVAR_ML1_VISAL_010 *I251FML1_VISAL  ---  ---AI218F
15UniProtVAR_ML1_VISAL_017 *G524YML1_VISAL  ---  ---BG223Y
16UniProtVAR_ML1_VISAL_018 *N531SML1_VISAL  ---  ---BN230S
17UniProtVAR_ML1_VISAL_019 *N531TML1_VISAL  ---  ---BN230T
18UniProtVAR_ML1_VISAL_011 *T264SML1_VISAL  ---  ---AT231S
19UniProtVAR_ML1_VISAL_012 *D268SML1_VISAL  ---  ---AD235S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (19, 19)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_ML1_VISAL_001 *E48DML1_VISAL  ---  ---AD15D
02UniProtVAR_ML1_VISAL_013 *N319SML1_VISAL  ---  ---BN18S
03UniProtVAR_ML1_VISAL_014 *G357NML1_VISAL  ---  ---BG56N
04UniProtVAR_ML1_VISAL_002 *N145TML1_VISAL  ---  ---AN112T
05UniProtVAR_ML1_VISAL_003 *P149TML1_VISAL  ---  ---AP116T
06UniProtVAR_ML1_VISAL_004 *T173SML1_VISAL  ---  ---AT140S
07UniProtVAR_ML1_VISAL_005 *F177YML1_VISAL  ---  ---AF144Y
08UniProtVAR_ML1_VISAL_006 *T184AML1_VISAL  ---  ---AT151A
09UniProtVAR_ML1_VISAL_015 *G458QML1_VISAL  ---  ---BG157Q
10UniProtVAR_ML1_VISAL_007 *Y212DML1_VISAL  ---  ---AY179D
11UniProtVAR_ML1_VISAL_008 *A217EML1_VISAL  ---  ---AA184E
12UniProtVAR_ML1_VISAL_009 *V223MML1_VISAL  ---  ---AV190M
13UniProtVAR_ML1_VISAL_016 *C495VML1_VISAL  ---  ---BC194V
14UniProtVAR_ML1_VISAL_010 *I251FML1_VISAL  ---  ---AI218F
15UniProtVAR_ML1_VISAL_017 *G524YML1_VISAL  ---  ---BG223Y
16UniProtVAR_ML1_VISAL_018 *N531SML1_VISAL  ---  ---BN230S
17UniProtVAR_ML1_VISAL_019 *N531TML1_VISAL  ---  ---BN230T
18UniProtVAR_ML1_VISAL_011 *T264SML1_VISAL  ---  ---AT231S
19UniProtVAR_ML1_VISAL_012 *D268SML1_VISAL  ---  ---AD235S
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.ML1_VISAL309-436
440-563		  2B:8-135
B:139-262
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.ML1_VISAL309-436
440-563		  4B:8-135
B:139-262
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RICIN_B_LECTINPS50231 Lectin domain of ricin B chain profile.ML1_VISAL309-436
440-563		  2B:8-135
B:139-262

(-) Exons   (0, 0)

(no "Exon" information available for 1OQL)

(-) 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)
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:248
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:248
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273        
            ML1_VISAL    34 YERLRLRVTHQTTGEEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNEGGDSITAAIDVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQQSTDGVFNNPIRLAIPPGNFVTLTNVRDVIASLAIMLFVCG 281
               SCOP domains d1oqla_ A: Mistletoe lectin I A-chain                                                                                                                                                                                                                    SCOP domains
               CATH domains 1oqlA01 A:1-167 Ricin (A subunit), domain 1                                                                                                                            1oqlA02 A:168-248 Ricin (A Subunit), domain 2                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhheeeeee..eeee............eeeeeeee....eeeeeee.....eeeeee..eeeeee....hhhhhh.......eeeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeeee...eeeeeee.hhh............ Sec.struct. author
                 SAPs(SNPs) --------------D------------------------------------------------------------------------------------------------T---T-----------------------S---Y------A---------------------------D----E-----M---------------------------F------------S---S------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oql A   1 YERLRLRVTHQTTGDEYFRFITLLRDYVSSGSFSNEIPLLRQSTIPVSDAQRFVLVELTNQGGDSITAAIDVTNLYVVAYQAGDQSYFLRDAPRGAETHLFTGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIRLAIPPGNFVTLTNVRDVIASLAIMLFVCG 248
                                    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:263
 aligned with ML1_VISAL | P81446 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:263
                                   311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561   
            ML1_VISAL   302 DDVTCSASEPTVRIVGRNGMCVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVISQQNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGKPNQMWLPVP 564
               SCOP domains d1oqlb1 B:1-137 Plant cytotoxin B-chain (lectin)                                                                                         d1oqlb2 B:138-263 Plant cytotoxin B-chain (lectin)                                                                             SCOP domains
               CATH domains 1oqlB01 B:1-139  [code=2.80.10.50, no name defined]                                                                                        1oqlB02 B:140-263  [code=2.80.10.50, no name defined]                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeee..........eee....hhhhh.ee......eeeeeehhhhheeeee..eeeee.....hhhh.eee.....eee.....eeee..........eeee....hhhh.eee.....eee.....eeee.hhhhhhh.eeee....hhhhh.eee. 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:8-135 UniProt: 309-436                                                                                   ---RICIN_B_LECTIN  PDB: B:139-262 UniProt: 440-563                                                                             - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1oql B   1 DDVTCSASEPTVRIVGRNGMCVDVRDDDFRDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESNGGSVWVETCVSSQKNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPKLRRIIIYPATGKPNQMWLPVP 263
                                    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       260
   Legend:   → Mismatch (orange background)
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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  (2, 3)

Asymmetric Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Few Secondary Structures (1120)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1OQL)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,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.

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  ML1_VISAL | P81446
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ML1_VISAL | P81446: 1ce7 1m2t 1onk 1pum 1puu 1sz6 2mll 2r9k 2rg9 3d7w 3o5w 4eb2 4jkx

(-) Related Entries Specified in the PDB File

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