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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 :  3.40
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E  (2x)
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, E
    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

  12345
Asymmetric Unit : ABCDE
Biological Unit 1 (1x): AB   
Biological Unit 2 (1x):   CD 
Biological Unit 3 (2x):     E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1MMA6Ligand/IonO1-METHYL-MANNOSE
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MMA3Ligand/IonO1-METHYL-MANNOSE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MMA2Ligand/IonO1-METHYL-MANNOSE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1MMA2Ligand/IonO1-METHYL-MANNOSE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN B:29 , ASP B:31 , ASN B:33 , TYR B:37 , PRO C:72 , VAL C:73BINDING SITE FOR RESIDUE MMA B 201
2AC2SOFTWAREPRO A:72 , GLN B:59 , ASP B:61 , ASN B:63 , TYR B:67BINDING SITE FOR RESIDUE MMA B 202
3AC3SOFTWAREGLN B:89 , ASP B:91 , ASN B:93 , TYR B:97 , PRO B:102 , SER B:105BINDING SITE FOR RESIDUE MMA B 203
4AC4SOFTWAREPRO B:72 , VAL B:73 , HIS B:75 , GLN C:29 , ASP C:31 , ASN C:33 , TYR C:37 , ALA C:42BINDING SITE FOR RESIDUE MMA C 201
5AC5SOFTWARELYS C:10 , GLN C:89 , ASP C:91 , ASN C:93 , TYR C:97BINDING SITE FOR RESIDUE MMA C 202
6AC6SOFTWAREGLN A:29 , TYR A:37 , GLN E:29 , ASP E:31 , ASN E:33 , VAL E:35 , TYR E:37 , SER E:45 , ASN E:49BINDING SITE FOR RESIDUE MMA E 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OIZ)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee...eee...eee.....eeeee.....eeeee...eeee.......eeeeee.....eeeee..eeeee.........eeee.....eeee....eeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4oiz A   1 MGDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLE 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain B from PDB  Type:PROTEIN  Length:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eee...eee......eeee.....eeee....eeee.......eeeeee.....eeeee...eeee.........eeee.....eeeee..eeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 4oiz B   1 MGDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLE 107
                                    10        20        30        40        50        60        70        80        90       100       


Chain C 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
                 4oiz C   1 MGDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSLE 107
                                    10        20        30        40        50        60        70        80        90       100       


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......eeee.....eeeee..eeeee.......eeeeee.....eeeee..eeeee.........eeee.....eeee....eee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------- Transcript
                 4oiz D   1 MGDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSL 106
                                    10        20        30        40        50        60        70        80        90       100      


Chain E from PDB  Type:PROTEIN  Length:105
                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee...eee......eeee.....eeee....eeee.......eeeeee.....eeeee................eeee.....eeee....eee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 4oiz E   2 GDTLTAGQKLERGGSLQSGNGAYTLTLQDDGNLVLYARDKAVWSTGTNGQDVVRAEVQTDGNFVLYTAEKPVWHTDTKGKKEVKLVLQDDRNLVLYAKDGPAWSL 106
                                    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 4OIZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

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        A0QYH7_MYCS2 | A0QYH7: 4oit 4okc

(-) Related Entries Specified in the PDB File

4oit THE SAME PROTEIN COMPLEXED WITH MANNOSE.