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(-) Description

Title :  STRUCTURE, INTERACTIONS AND EVOLUTIONARY IMPLICATIONS OF A DOMAIN-SWAPPED LECTIN DIMER FROM MYCOBACTERIUM SMEGMATIS
 
Authors :  D. Patra, P. Mishra, A. Surolia, M. Vijayan
Date :  20 Jan 14  (Deposition) - 23 Jul 14  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Beta-Prism Ii Fold, Bacterial Lectin, Protein-Carbohydrate Interactions, Beta-Prism Ii, Carbohydrate Binding, Carbohydrate/Sugar, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Patra, P. Mishra, A. Surolia, M. Vijayan
Structure, Interactions And Evolutionary Implications Of A Domain-Swapped Lectin Dimer From Mycobacterium Smegmatis
Glycobiology 2014
PubMed-ID: 24957055  |  Reference-DOI: 10.1093/GLYCOB/CWU059
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LYSM DOMAIN PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: MANNOSE-BINDING LECTIN DOMAIN, UNP RESIDUES 1-105
    Gene: MSMEG_3662
    Organism Scientific: MYCOBACTERIUM SMEGMATIS
    Organism Taxid: 246196
    Strain: MC2 155
    Synonym: MANNOSE-BINDING LECTIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN10Ligand/IonALPHA-D-MANNOSE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN4Ligand/IonALPHA-D-MANNOSE
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1BMA-1Ligand/IonBETA-D-MANNOSE
2MAN6Ligand/IonALPHA-D-MANNOSE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:29 , ASP A:31 , ASN A:33 , TYR A:37 , ASN A:49 , HOH A:317 , VAL C:73BINDING SITE FOR RESIDUE MAN A 201
02AC2SOFTWAREGLN A:59 , ASP A:61 , ASN A:63 , TYR A:67 , PRO B:72BINDING SITE FOR RESIDUE MAN A 202
03AC3SOFTWAREGLN A:89 , ASP A:91 , ASN A:93 , TYR A:97 , SER A:105BINDING SITE FOR RESIDUE MAN A 203
04AC4SOFTWAREGLN B:89 , ASP B:91 , ASN B:93 , TYR B:97 , SER B:105BINDING SITE FOR RESIDUE MAN B 201
05AC5SOFTWAREPRO A:72 , HIS A:75 , LYS A:79 , GLN B:59 , ASP B:61 , ASN B:63 , TYR B:67 , MAN C:201BINDING SITE FOR RESIDUE BMA B 202
06AC6SOFTWAREVAL A:73 , HOH A:335 , BMA B:202 , GLN C:29 , ASP C:31 , ASN C:33 , TYR C:37 , ALA C:42 , SER C:45 , ASN C:49BINDING SITE FOR RESIDUE MAN C 201
07AC7SOFTWAREGLN C:89 , ASP C:91 , ASN C:93 , TYR C:97 , SER C:105 , HOH C:307BINDING SITE FOR RESIDUE MAN C 202
08AC8SOFTWAREGLN C:59 , ASP C:61 , ASN C:63 , TYR C:67 , LYS D:79BINDING SITE FOR RESIDUE MAN C 203
09AC9SOFTWAREGLN D:29 , ASP D:31 , ASN D:33 , TYR D:37BINDING SITE FOR RESIDUE MAN D 201
10BC1SOFTWAREGLN D:89 , ASP D:91 , ASN D:93 , TYR D:97 , SER D:105 , HOH D:309 , HOH D:310 , HOH D:311BINDING SITE FOR RESIDUE MAN D 202
11BC2SOFTWAREASP B:40 , HIS C:75 , GLN D:59 , ASP D:61 , ASN D:63 , TYR D:67 , HOH D:332BINDING SITE FOR RESIDUE MAN D 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OIT)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4OIT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OIT)

(-) 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:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee...eeee....eeeee.....eeeee..eeeee.......eeeeee.....eeeee...eeee.........eeee.....eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4oit A   2 GDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLE 107
                                    11        21        31        41        51        61        71        81        91       101      


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee...eee.....eeeee.....eeeee..eeeee.......eeeeee.....eeeee...eeee.........eeee.....eeeee..eeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4oit B   2 GDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLEH 108
                                    11        21        31        41        51        61        71        81        91       101       


Chain C from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee...eee.....eeeee.....eeeee..eeeee.......eeeeee.....eeeee...eeee.........eeee.....eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4oit C   2 GDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLE 107
                                    11        21        31        41        51        61        71        81        91       101      


Chain D from PDB  Type:PROTEIN  Length:106
                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...eee...eee.....eeeee.....eeeee..eeeee.......eeeeee.....eeeee..eeeee.........eeee.....eeeee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4oit D   2 GDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLE 107
                                    11        21        31        41        51        61        71        81        91       101
   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  (0, 0)

(no "SCOP Domain" information available for 4OIT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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        A0QYH7_MYCS2 | A0QYH7: 4oiz 4okc

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