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(-) Description

Title :  FV M6P-1 IN COMPLEX WITH MANNOSE-6-PHOSPHATE
 
Authors :  R. J. Blackler, D. W. Evans, S. V. Evans, S. Muller-Loennies
Date :  19 Dec 14  (Deposition) - 04 Nov 15  (Release) - 05 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.72
Chains :  Asym. Unit :  A,B,C,D,E,F,H,L
Biol. Unit 1:  H,L  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Antibody Variable Fragment, Mannose-6-Phosphate, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Blackler, D. W. Evans, D. F. Smith, R. D. Cummings, C. L. Brooks, T. Braulke, X. Liu, S. V. Evans, S. Muller-Loennies
Single-Chain Antibody-Fragment M6P-1 Possesses A Mannose 6-Phosphate Monosaccharide-Specific Binding Pocket That Distinguishes N-Glycan Phosphorylation In A Branch-Specific Manner.
Glycobiology V. 26 181 2016
PubMed-ID: 26503547  |  Reference-DOI: 10.1093/GLYCOB/CWV093

(-) Compounds

Molecule 1 - FV M6P-1 LIGHT CHAIN
    Chains: H, A, C, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSJF8
    Expression System Strain: TG-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986
 
Molecule 2 - FV M6P-1 HEAVY CHAIN
    Chains: L, B, D, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSJF8
    Expression System Strain: TG-1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ORYCTOLAGUS CUNICULUS
    Organism Taxid: 9986

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFHL
Biological Unit 1 (1x):       HL
Biological Unit 2 (1x): AB      
Biological Unit 3 (1x):   CD    
Biological Unit 4 (1x):     EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1M6P4Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1M6P1Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1M6P1Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1M6P1Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1M6P1Ligand/IonALPHA-D-MANNOSE-6-PHOSPHATE
2SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP H:31 , THR H:33 , ASP H:95 , ILE H:97 , ASN H:98 , ARG L:32 , ARG L:95CBINDING SITE FOR RESIDUE M6P H 201
02AC2SOFTWAREGLN L:42 , ARG L:43 , HOH L:321BINDING SITE FOR RESIDUE SO4 L 201
03AC3SOFTWARETRP A:31 , THR A:33 , ASP A:95 , ILE A:97 , ASN A:98 , ARG B:32 , ARG B:95CBINDING SITE FOR RESIDUE M6P A 201
04AC4SOFTWAREGLN B:42 , ARG B:43BINDING SITE FOR RESIDUE SO4 B 201
05AC5SOFTWARETRP C:31 , TYR C:32 , THR C:33 , ASP C:95 , GLY C:96 , ILE C:97 , ASN C:98 , HOH C:312 , HOH C:320 , HOH C:322 , ARG D:32 , ARG D:95CBINDING SITE FOR RESIDUE M6P C 201
06AC6SOFTWAREGLN D:42 , ARG D:43 , SER L:56BINDING SITE FOR RESIDUE SO4 D 201
07AC7SOFTWAREARG D:95CBINDING SITE FOR RESIDUE SO4 D 202
08AC8SOFTWARETYR E:32 , THR E:33 , ASP E:95 , GLY E:96 , ILE E:97 , ASN E:98 , HOH E:327 , ARG F:32 , ARG F:95CBINDING SITE FOR RESIDUE M6P E 201
09AC9SOFTWARESER B:56 , GLN F:42 , ARG F:43BINDING SITE FOR RESIDUE SO4 F 201
10BC1SOFTWAREARG F:95CBINDING SITE FOR RESIDUE SO4 F 202

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:22 -A:92
2B:23 -B:88
3C:22 -C:92
4D:23 -D:88
5E:22 -E:92
6F:23 -F:88
7H:22 -H:92
8L:23 -L:88

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Gly L:68 -Thr L:69
2Thr B:7 -Glu B:8
3Gly B:68 -Thr B:69
4Gly D:68 -Thr D:69
5Ser D:94 -Asn D:95
6Gly F:68 -Thr F:69
7Ser F:94 -Asn F:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RZC)

(-) 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:119
                                                                                                                                                        
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.......eee.hhhh..eeeeeee..eeeeee...hhhhheeeeeeee.......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                4rzc A    0 ASQSVKESEGDLVKPGASLTLTCKASGFDFTWYTMNWVRQAPGKGLEWIASIGAGVYGSNYYASWAKGRFTISKASSTTVTLQMTSLTVADTATYFCARDGINGGYDIWGPGTLVTVSS  113
                                     9        19        29        39        49   ||   57        67        77     || 85        95     | 104         
                                                                               52A|                            82A|               100A             
                                                                                52B                             82B                                


Chain B from PDB  Type:PROTEIN  Length:109
                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....eee....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee.....eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                4rzc B    2 LVMTQTESPVSAAGGTVTIKCQSSQSVYNNRLAWYQQKPGQRPKLLIYSASTLASGVPSRFKGSGSGTQFTLTISDLEWGDAATYYCHGGYRSDRYAFSGGTELEILSS  108
                                    11  ||    22     |  31        41        51        61        71        81        91   ||  100      |  
                                       14|         27A                                                                 95B|        106A  
                                        16                                                                              95C              


Chain C from PDB  Type:PROTEIN  Length:117
                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.......eee.hhhh..eeeeeee..eeeeee...hhhhheeeeeeee.......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                4rzc C    2 QSVKESEGDLVKPGASLTLTCKASGFDFTWYTMNWVRQAPGKGLEWIASIGAGVYGSNYYASWAKGRFTISKASSTTVTLQMTSLTVADTATYFCARDGINGGYDIWGPGTLVTVSS  113
                                    11        21        31        41        51 ||     59        69        79   ||   87        97   |   106       
                                                                             52A|                            82A|               100A             
                                                                              52B                             82B                                


Chain D from PDB  Type:PROTEIN  Length:111
                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eee....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                4rzc D    2 LVMTQTESPVSAAGGTVTIKCQSSQSVYNNRLAWYQQKPGQRPKLLIYSASTLASGVPSRFKGSGSGTQFTLTISDLEWGDAATYYCHGGYRSNDDRYAFSGGTELEILSS  108
                                    11  ||    22     |  31        41        51        61        71        81        91    ||| 98       107 
                                       14|         27A                                                                  95A||        106A  
                                        16                                                                               95B|              
                                                                                                                          95C              


Chain E from PDB  Type:PROTEIN  Length:117
                                                                                                                                                      
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.......eee.hhhh..eeeeeee..eeeeee...hhhhheeeeeeee.......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                4rzc E    2 QSVKESEGDLVKPGASLTLTCKASGFDFTWYTMNWVRQAPGKGLEWIASIGAGVYGSNYYASWAKGRFTISKASSTTVTLQMTSLTVADTATYFCARDGINGGYDIWGPGTLVTVSS  113
                                    11        21        31        41        51 ||     59        69        79   ||   87        97   |   106       
                                                                             52A|                            82A|               100A             
                                                                              52B                             82B                                


Chain F from PDB  Type:PROTEIN  Length:111
                                                                                                                                                
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eee....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee.......eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                4rzc F    2 LVMTQTESPVSAAGGTVTIKCQSSQSVYNNRLAWYQQKPGQRPKLLIYSASTLASGVPSRFKGSGSGTQFTLTISDLEWGDAATYYCHGGYRSNDDRYAFSGGTELEILSS  108
                                    11  ||    22     |  31        41        51        61        71        81        91    ||| 98       107 
                                       14|         27A                                                                  95A||        106A  
                                        16                                                                               95B|              
                                                                                                                          95C              


Chain H from PDB  Type:PROTEIN  Length:118
                                                                                                                                                       
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...ee.....eeeeeeee.......eeeeeee.....eeeeeee.......eee.hhhh..eeeeeee..eeeeee...hhhhheeeeeeee.......ee...eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                4rzc H    1 SQSVKESEGDLVKPGASLTLTCKASGFDFTWYTMNWVRQAPGKGLEWIASIGAGVYGSNYYASWAKGRFTISKASSTTVTLQMTSLTVADTATYFCARDGINGGYDIWGPGTLVTVSS  113
                                    10        20        30        40        50  ||    58        68        78    ||  86        96    |  105        
                                                                              52A|                            82A|               100A             
                                                                               52B                             82B                                


Chain L from PDB  Type:PROTEIN  Length:110
                                                                                                                                               
               SCOP domains -------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.....eee....eeeeeee........eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhheeeeeeee......eee...eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------- Transcript
                4rzc L    2 LVMTQTESPVSAAGGTVTIKCQSSQSVYNNRLAWYQQKPGQRPKLLIYSASTLASGVPSRFKGSGSGTQFTLTISDLEWGDAATYYCHGGYRNDDRYAFSGGTELEILSS  108
                                    11  ||    22     |  31        41        51        61        71        81        91 |||||  99       108
                                       14|         27A                                                                93||||        106A  
                                        16                                                                             95|||              
                                                                                                                       95A||              
                                                                                                                        95B|              
                                                                                                                         95C
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  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 4RZC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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  4rzc
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