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(-) Description

Title :  CRYSTAL STRUCTURE OF A PLATELET AGGLUTINATION FACTOR ISOLATED FROM THE VENOM OF TAIWAN HABU (TRIMERESURUS MUCROSQUAMATUS)
 
Authors :  K. -F. Huang, T. -P. Ko, A. H. -J. Wang
Date :  14 Nov 03  (Deposition) - 02 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C,D,E,F  (4x)
Biol. Unit 2:  E,F  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  C,D  (1x)
Biol. Unit 5:  A,B,C,D  (4x)
Biol. Unit 6:  E,F  (8x)
Keywords :  Lectin-Like, Square-Shaped Ring, Blood Clotting (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. F. Huang, T. P. Ko, C. C. Hung, J. Chu, A. H. Wang, S. H. Chiou
Crystal Structure Of A Platelet-Agglutinating Factor Isolated From The Venom Of Taiwan Habu (Trimeresurus Mucrosquamatus).
Biochem. J. V. 378 399 2004
PubMed-ID: 14613481  |  Reference-DOI: 10.1042/BJ20031507

(-) Compounds

Molecule 1 - MUCROCETIN ALPHA CHAIN
    ChainsA, C, E
    Organism ScientificPROTOBOTHROPS MUCROSQUAMATUS
    Organism Taxid103944
    SecretionSNAKE VENOM
 
Molecule 2 - MUCROCETIN BETA CHAIN
    ChainsB, D, F
    Organism ScientificPROTOBOTHROPS MUCROSQUAMATUS
    Organism Taxid103944
    SecretionSNAKE VENOM

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (4x)ABCDEF
Biological Unit 2 (1x)    EF
Biological Unit 3 (1x)AB    
Biological Unit 4 (1x)  CD  
Biological Unit 5 (4x)ABCD  
Biological Unit 6 (8x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1V4L)

(-) Sites  (0, 0)

(no "Site" information available for 1V4L)

(-) SS Bonds  (24, 24)

Asymmetric Unit
No.Residues
1A:4 -A:15
2A:32 -A:129
3A:81 -B:277
4A:104 -A:121
5A:135 -B:203
6B:204 -B:215
7B:232 -B:321
8B:298 -B:313
9C:4 -C:15
10C:32 -C:129
11C:81 -D:277
12C:104 -C:121
13C:135 -D:203
14D:204 -D:215
15D:232 -D:321
16D:298 -D:313
17E:4 -E:15
18E:32 -E:129
19E:81 -F:277
20E:104 -E:121
21E:135 -F:203
22F:204 -F:215
23F:232 -F:321
24F:298 -F:313

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1V4L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V4L)

(-) PROSITE Motifs  (2, 12)

Asymmetric Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  3A:11-130
C:11-130
E:11-130
SLOB_PROMU34-145
 
 
  3B:211-322
D:211-322
F:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  3B:298-321
D:298-321
F:298-321
SLOA_PROMU127-152
 
 
  3A:104-129
C:104-129
E:104-129
Biological Unit 1 (2, 48)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  12A:11-130
C:11-130
E:11-130
SLOB_PROMU34-145
 
 
  12B:211-322
D:211-322
F:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  12B:298-321
D:298-321
F:298-321
SLOA_PROMU127-152
 
 
  12A:104-129
C:104-129
E:104-129
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  1-
-
E:11-130
SLOB_PROMU34-145
 
 
  1-
-
F:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  1-
-
F:298-321
SLOA_PROMU127-152
 
 
  1-
-
E:104-129
Biological Unit 3 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  1A:11-130
-
-
SLOB_PROMU34-145
 
 
  1B:211-322
-
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  1B:298-321
-
-
SLOA_PROMU127-152
 
 
  1A:104-129
-
-
Biological Unit 4 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  1-
C:11-130
-
SLOB_PROMU34-145
 
 
  1-
D:211-322
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  1-
D:298-321
-
SLOA_PROMU127-152
 
 
  1-
C:104-129
-
Biological Unit 5 (2, 32)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  8A:11-130
C:11-130
-
SLOB_PROMU34-145
 
 
  8B:211-322
D:211-322
-
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  8B:298-321
D:298-321
-
SLOA_PROMU127-152
 
 
  8A:104-129
C:104-129
-
Biological Unit 6 (2, 32)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1C_TYPE_LECTIN_2PS50041 C-type lectin domain profile.SLOA_PROMU34-153
 
 
  8-
-
E:11-130
SLOB_PROMU34-145
 
 
  8-
-
F:211-322
2C_TYPE_LECTIN_1PS00615 C-type lectin domain signature.SLOB_PROMU121-144
 
 
  8-
-
F:298-321
SLOA_PROMU127-152
 
 
  8-
-
E:104-129

(-) Exons   (0, 0)

(no "Exon" information available for 1V4L)

(-) 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:135
 aligned with SLOA_PROMU | Q6TPH0 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:135
                                    33        43        53        63        73        83        93       103       113       123       133       143       153     
           SLOA_PROMU    24 DFDCIPGWSAYDRYCYQAFSEPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLYKQSSKKCYALKKGTELRTWFNVYCGRENPFVCKYTPEC 158
               SCOP domains d1v4la_ A: Snake coagglutinin alpha chain                                                                                               SCOP domains
               CATH domains 1v4lA00 A:1-135 Mannose-Binding Protein A, subunit A                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhh...eee....hhhhhhhhhhhhhh.......eeeeeeee......................hhhhh..eeeee........eee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------C_TYPE_LECTIN_2  PDB: A:11-130 UniProt: 34-153                                                                          ----- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ------ PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4l A   1 DFDCIPGWSAYDRYCYQAFSEPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLYKQSSKKCYALKKGTELRTWFNVYCGRENPFVCKYTPEC 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     

Chain B from PDB  Type:PROTEIN  Length:125
 aligned with SLOB_PROMU | Q6TPG9 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    33        43        53        63        73        83        93       103       113       123       133       143     
           SLOB_PROMU    24 GFCCPLGWSSYDEHCYQVFQQKINWEDAEKFCTQQHRGSHLVSFHSSEEVDFVVSKTSPILKHDFVWMGLSNVWNECAKEWSDGTKLDYKAWSGQSDCITSKTTDNQWLSMDCSSKRYVVCKFQA 148
               SCOP domains d1v4lb_ B: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1v4lB00 B:201-325 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhhh..eee....hhhhhhhhhhhhh......eee...........eee...............eeeeee.....eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: B:211-322 UniProt: 34-145                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4l B 201 GFCCPLGWSSYDEHCYQVFQQKMNWEDAEKFCTQQHRGSHLVSFHSSEEVDFVVSKTSPILKHDFVWMGLSNVWNECAKEWSDGTKLDYKAWSGQSDCITSKTTDNQWLSMDCSSKRYVVCKFQA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320     

Chain C from PDB  Type:PROTEIN  Length:135
 aligned with SLOA_PROMU | Q6TPH0 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:135
                                    33        43        53        63        73        83        93       103       113       123       133       143       153     
           SLOA_PROMU    24 DFDCIPGWSAYDRYCYQAFSEPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLYKQSSKKCYALKKGTELRTWFNVYCGRENPFVCKYTPEC 158
               SCOP domains d1v4lc_ C: Snake coagglutinin alpha chain                                                                                               SCOP domains
               CATH domains 1v4lC00 C:1-135 Mannose-Binding Protein A, subunit A                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.....eeeeeeee......................hhhhh..eeeee.......eeee.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------C_TYPE_LECTIN_2  PDB: C:11-130 UniProt: 34-153                                                                          ----- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ------ PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4l C   1 DFDCIPGWSAYDRYCYQAFSEPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLYKQSSKKCYALKKGTELRTWFNVYCGRENPFVCKYTPEC 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     

Chain D from PDB  Type:PROTEIN  Length:125
 aligned with SLOB_PROMU | Q6TPG9 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    33        43        53        63        73        83        93       103       113       123       133       143     
           SLOB_PROMU    24 GFCCPLGWSSYDEHCYQVFQQKINWEDAEKFCTQQHRGSHLVSFHSSEEVDFVVSKTSPILKHDFVWMGLSNVWNECAKEWSDGTKLDYKAWSGQSDCITSKTTDNQWLSMDCSSKRYVVCKFQA 148
               SCOP domains d1v4ld_ D: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1v4lD00 D:201-325 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhhh...ee.....hhhhhhhhhhhh....................eee...............eee..........eee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: D:211-322 UniProt: 34-145                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4l D 201 GFCCPLGWSSYDEHCYQVFQQKMNWEDAEKFCTQQHRGSHLVSFHSSEEVDFVVSKTSPILKHDFVWMGLSNVWNECAKEWSDGTKLDYKAWSGQSDCITSKTTDNQWLSMDCSSKRYVVCKFQA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320     

Chain E from PDB  Type:PROTEIN  Length:135
 aligned with SLOA_PROMU | Q6TPH0 from UniProtKB/Swiss-Prot  Length:158

    Alignment length:135
                                    33        43        53        63        73        83        93       103       113       123       133       143       153     
           SLOA_PROMU    24 DFDCIPGWSAYDRYCYQAFSEPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLYKQSSKKCYALKKGTELRTWFNVYCGRENPFVCKYTPEC 158
               SCOP domains d1v4le_ E: Snake coagglutinin alpha chain                                                                                               SCOP domains
               CATH domains 1v4lE00 E:1-135 Mannose-Binding Protein A, subunit A                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeeehhhhhhhh......eee....hhhhhhhhhhhhhhhh.....eeeeeeee.............................eeeee.......eeee....eeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) ----------C_TYPE_LECTIN_2  PDB: E:11-130 UniProt: 34-153                                                                          ----- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ------ PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4l E   1 DFDCIPGWSAYDRYCYQAFSEPKNWEDAESFCEEGVKTSHLVSIESSGEGDFVAQLVAEKIKTSFQYVWIGLRIQNKEQQCRSEWSDASSVNYENLYKQSSKKCYALKKGTELRTWFNVYCGRENPFVCKYTPEC 135
                                    10        20        30        40        50        60        70        80        90       100       110       120       130     

Chain F from PDB  Type:PROTEIN  Length:125
 aligned with SLOB_PROMU | Q6TPG9 from UniProtKB/Swiss-Prot  Length:148

    Alignment length:125
                                    33        43        53        63        73        83        93       103       113       123       133       143     
           SLOB_PROMU    24 GFCCPLGWSSYDEHCYQVFQQKINWEDAEKFCTQQHRGSHLVSFHSSEEVDFVVSKTSPILKHDFVWMGLSNVWNECAKEWSDGTKLDYKAWSGQSDCITSKTTDNQWLSMDCSSKRYVVCKFQA 148
               SCOP domains d1v4lf_ F: Snake coagglutinin beta chain                                                                                      SCOP domains
               CATH domains 1v4lF00 F:201-325 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eee..eeeeeeeeeehhhhhhhhhhhhh...ee....hhhhhhhhhhhhh......eee...........eee...............eeeeee.....eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------C_TYPE_LECTIN_2  PDB: F:211-322 UniProt: 34-145                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (3)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v4l F 201 GFCCPLGWSSYDEHCYQVFQQKMNWEDAEKFCTQQHRGSHLVSFHSSEEVDFVVSKTSPILKHDFVWMGLSNVWNECAKEWSDGTKLDYKAWSGQSDCITSKTTDNQWLSMDCSSKRYVVCKFQA 325
                                   210       220       230       240       250       260       270       280       290       300       310       320     

   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, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V4L)

(-) Gene Ontology  (1, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,C,E   (SLOA_PROMU | Q6TPH0)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain B,D,F   (SLOB_PROMU | Q6TPG9)
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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  1v4l
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 Related Entries

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