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(-) Description

Title :  CRYSTAL STRUCTURE MISTLETOE LECTIN I FROM VISCUM ALBUM IN COMPLEX WITH N-ACETYL-D-GLUCOSAMINE AT 1.94 A RESOLUTION.
 
Authors :  A. A. Laskov, I. I. Prokofev, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikha
Date :  23 Mar 12  (Deposition) - 27 Mar 13  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  A,B  (1x)
Keywords :  Rossmann Fold, Ribosome-Inactivating Protein Type Ii, Glycoprotein, Plant Defense, Protein Synthesis Inhibitor, Toxin, Sarcin/Ricin Domain, Galactose Binding Receptor, Hydrolase-Sugar Binding Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. A. Laskov, I. I. Prokofev, A. G. Gabdoulkhakov, C. Betzel, A. M. Mikhailov
Crystal Structure Mistletoe Lectin I From Viscum Album In Complex With N-Acetyl-D-Glucosamine At 1. 94 A Resolution.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BETA-GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN A
    Chains: A
    EC Number: 3.2.2.22
    Fragment: SEE REMARK 999
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Synonym: VISCUMIN, BETA-GALACTOSIDE-SPECIFIC LECTIN I CHAIN A, ML-I A, MLA, RRNA N-GLYCOSIDASE
 
Molecule 2 - BETA-GALACTOSIDE-SPECIFIC LECTIN 1 CHAIN B
    Chains: B
    Fragment: SEE REMARK 999
    Organism Common: EUROPEAN MISTLETOE
    Organism Scientific: VISCUM ALBUM
    Organism Taxid: 3972
    Synonym: VISCUMIN, BETA-GALACTOSIDE-SPECIFIC LECTIN I CHAIN B, ML-I B, MLB

 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  (7, 28)

Asymmetric Unit (7, 28)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2CL1Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4GOL7Ligand/IonGLYCEROL
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
7SO42Ligand/IonSULFATE ION
Biological Unit 1 (6, 54)
No.NameCountTypeFull Name
1AZI2Ligand/IonAZIDE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO10Ligand/Ion1,2-ETHANEDIOL
4GOL14Ligand/IonGLYCEROL
5NAG10Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PEG14Ligand/IonDI(HYDROXYETHYL)ETHER
7SO44Ligand/IonSULFATE ION
Biological Unit 2 (6, 27)
No.NameCountTypeFull Name
1AZI1Ligand/IonAZIDE ION
2CL-1Ligand/IonCHLORIDE ION
3EDO5Ligand/Ion1,2-ETHANEDIOL
4GOL7Ligand/IonGLYCEROL
5NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE
6PEG7Ligand/IonDI(HYDROXYETHYL)ETHER
7SO42Ligand/IonSULFATE ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:91 , ASN A:112 , SER A:114 , ASP A:117BINDING SITE FOR RESIDUE NAG A 301
02AC2SOFTWARETYR A:115 , GLU A:119 , HIS A:124 , ARG A:125 , ASP A:126BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREGLN A:205 , HIS A:208 , ASN A:216BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREGLN A:148 , THR A:149 , ARG A:150 , ASN B:105BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREPRO A:171 , ARG A:175 , GLN A:178 , ASP B:150BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREGLY A:63 , ASP A:64 , SER A:65 , ARG A:143BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREARG A:175 , ASP A:189 , TYR B:146 , PRO B:263BINDING SITE FOR RESIDUE GOL A 307
08AC8SOFTWARETYR A:76 , GLY A:113 , TYR A:115 , ARG A:168BINDING SITE FOR RESIDUE EDO A 308
09AC9SOFTWAREALA A:15 , ASN A:181BINDING SITE FOR RESIDUE CL A 309
10BC1SOFTWARESER A:30 , ARG A:41 , GLN A:42BINDING SITE FOR RESIDUE PEG A 310
11BC2SOFTWAREGLY A:95 , GLU A:97BINDING SITE FOR RESIDUE PEG A 311
12BC3SOFTWAREGLN A:178 , TYR A:179 , SER A:182 , ALA A:184 , ASN B:82BINDING SITE FOR RESIDUE PEG A 313
13BC4SOFTWAREASP A:211 , LYS B:53 , LYS B:54 , GLY B:56BINDING SITE FOR RESIDUE AZI B 301
14BC5SOFTWAREHIS A:124 , ASP A:126 , HOH A:462BINDING SITE FOR RESIDUE PEG A 312
15BC6SOFTWAREASP B:27 , PHE B:29 , ASN B:61 , HOH B:526 , HOH B:527 , HOH B:528BINDING SITE FOR RESIDUE NAG B 302
16BC7SOFTWAREPRO A:217 , ILE B:11 , ASN B:44 , LEU B:49 , ASN B:136 , NAG B:304 , HOH B:547BINDING SITE FOR RESIDUE NAG B 303
17BC8SOFTWAREILE B:11 , ASN B:44 , NAG B:303BINDING SITE FOR RESIDUE NAG B 304
18BC9SOFTWAREASN B:96 , TYR B:126 , LEU B:228 , PEG B:314 , HOH B:438 , HOH B:558BINDING SITE FOR RESIDUE NAG B 305
19CC1SOFTWAREASP B:23 , VAL B:24 , ARG B:25 , ASP B:26 , GLN B:36 , TRP B:38 , LYS B:41 , ASN B:47 , HOH B:457 , HOH B:503BINDING SITE FOR RESIDUE GOL B 306
20CC2SOFTWAREGLN A:134 , SER A:185 , ALA B:84 , VAL B:85 , HOH B:421 , HOH B:450BINDING SITE FOR RESIDUE GOL B 307
21CC3SOFTWAREGLU B:87 , ARG B:103 , HOH B:420 , HOH B:473BINDING SITE FOR RESIDUE GOL B 308
22CC4SOFTWAREGLU B:142 , ARG B:173 , LYS B:185 , HOH B:495BINDING SITE FOR RESIDUE EDO B 309
23CC5SOFTWAREARG B:59 , GLY B:62 , HOH B:538BINDING SITE FOR RESIDUE EDO B 310
24CC6SOFTWARESER B:200 , ARG B:245 , ILE B:247BINDING SITE FOR RESIDUE EDO B 311
25CC7SOFTWAREGLN B:30 , ASP B:31 , HOH B:514BINDING SITE FOR RESIDUE EDO B 312
26CC8SOFTWAREASN B:18 , TYR B:177 , ARG B:183 , GLN B:188 , HOH B:546BINDING SITE FOR RESIDUE PEG B 313
27CC9SOFTWAREASN B:96 , NAG B:305BINDING SITE FOR RESIDUE PEG B 314
28DC1SOFTWAREARG B:59 , ASN B:82 , ARG B:86BINDING SITE FOR RESIDUE PEG B 315

(-) 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  (1, 1)

Asymmetric Unit
No.Residues
1Tyr A:115 -Pro A:116

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EB2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EB2)

(-) Exons   (0, 0)

(no "Exon" information available for 4EB2)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               SCOP domains d4eb2a_ A: automated matches                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhhhhhhheeeeee..eeee............eeeeeeee....eeeeeee.....eeeeee..eeee......hhhhh.....eeee.......hhhhhhhhhhhhh..hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh...eeeeeeeee.....eeeeeehhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb2 A   1 YERLSLRTVQQTTGAEYFSFITLLRDFVSSGSFSNQIPLLRQSTIPVSEGQRFVLVELTNAGGDSITAAIDVTNLYVVAYQAGRQSYFLKDAPAGAETQDFAGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIASVTALRFPGGQTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIALALSPGSVVTLTNVRDVIASLAIMLFVCGE 249
                                    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
                                                                                                                                                                                                                                                                                                       
               SCOP domains d4eb2b1 B:1-137 automated matches                                                                                                        d4eb2b2 B:138-263 automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........ee.eehhhhheeee.hhh......eeee......hhhhheee.....eee..eeeee........eeee.....hhhhhh.ee.....eee....eeee..........eee....hhhhh.ee......eeeeeehhh.eeeeee..eeeeee....hhh.eeee.....eee.....eeee..........eeee....hhhh.eee.....eee.....eeee.hhh.....eeee....hhhhh.eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eb2 B   1 DDVTCSASEPIVRIVGRNGMTVDVRDDDFQDGNQIQLWPSKSNNDPNQLWTIKKDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESAGGSVQVETCTAGQENQRWALYGDGSIRPKQNQSQCLTNGRDSVSTVINIVSCSAGSSGQRWVFTNAGAILNLKNGLAMDVAQANPALARIIIYPATGNPNQMWLPVP 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)
  - → 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EB2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EB2)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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  ML1_VISAL | P81446
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  3.2.2.22
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1m2t 1pum 1sz6