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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROSTATE-SPECIFIC WGA16 GLYCOPROTEIN LECTIN, FORM II
 
Authors :  E. Garenaux, M. Kanagawa, T. Tsuchiyama, K. Hori, T. Kanazawa, A. Goshi M. Chiba, H. Yasue, A. Ikeda, Y. Yamaguchi, C. Sato, K. Kitajima
Date :  26 Dec 13  (Deposition) - 31 Dec 14  (Release) - 25 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Biol. Unit 6:  F  (1x)
Biol. Unit 7:  A,E  (1x)
Biol. Unit 8:  B (1x),D (1x)
Biol. Unit 9:  C,F  (1x)
Keywords :  Beta-Prism-Fold, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Garenaux, M. Kanagawa, T. Tsuchiyama, K. Hori, T. Kanazawa, A. Goshima, M. Chiba, H. Yasue, A. Ikeda, Y. Yamaguchi, C. Sato, K. Kitajima
Discovery, Primary, And Crystal Structures And Capacitation-Related Properties Of A Prostate-Derived Heparin-Binding Protein Wga16 From Boar Sperm
J. Biol. Chem. V. 290 5484 2015
PubMed-ID: 25568322  |  Reference-DOI: 10.1074/JBC.M114.635268

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SUS SCROFA
    Organism Taxid: 9823

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A     
Biological Unit 2 (1x):  B    
Biological Unit 3 (1x):   C   
Biological Unit 4 (1x):    D  
Biological Unit 5 (1x):     E 
Biological Unit 6 (1x):      F
Biological Unit 7 (1x): A   E 
Biological Unit 8 (1x):  B (1x) D (1x)  
Biological Unit 9 (1x):   C  F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 24)

Asymmetric Unit (3, 24)
No.NameCountTypeFull Name
1DIO16Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL2Ligand/IonGLYCEROL
3SO46Ligand/IonSULFATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1DIO8Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1DIO-1Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 5 (2, 3)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 6 (2, 3)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 7 (3, 13)
No.NameCountTypeFull Name
1DIO10Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION
Biological Unit 8 (3, 4)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
Biological Unit 9 (2, 4)
No.NameCountTypeFull Name
1DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
2GOL-1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:47 , PRO A:48 , VAL A:49 , LEU A:51 , LYS A:53BINDING SITE FOR RESIDUE SO4 A 201
02AC2SOFTWARESER A:17 , GLY A:18 , ILE A:30 , TYR E:134BINDING SITE FOR RESIDUE DIO A 202
03AC3SOFTWARETYR A:28 , PHE A:29 , MET E:20 , TYR E:28 , PHE E:29BINDING SITE FOR RESIDUE DIO A 203
04AC4SOFTWARETYR A:140 , PHE C:120BINDING SITE FOR RESIDUE DIO A 204
05AC5SOFTWARETHR A:31 , SER A:64 , GLU A:65 , TYR A:67BINDING SITE FOR RESIDUE DIO A 205
06AC6SOFTWAREMET A:20 , PHE A:21 , GLY A:22 , GLY A:24 , LYS A:25 , GLY A:26 , TYR A:28 , GLN E:136BINDING SITE FOR RESIDUE DIO A 206
07AC7SOFTWARELYS A:33 , GLY A:38 , PRO A:152 , ARG A:153BINDING SITE FOR RESIDUE DIO A 207
08AC8SOFTWAREGLN A:136 , TRP A:138 , THR A:143 , GLY C:106BINDING SITE FOR RESIDUE DIO A 208
09AC9SOFTWAREARG A:107BINDING SITE FOR RESIDUE DIO A 209
10BC1SOFTWAREALA A:121 , ALA A:122 , PHE A:147 , TRP A:149 , PHE E:21BINDING SITE FOR RESIDUE GOL A 210
11BC2SOFTWAREGLY B:47 , PRO B:48 , VAL B:49 , LYS B:53BINDING SITE FOR RESIDUE SO4 B 201
12BC3SOFTWAREPHE B:29 , ILE B:30 , PHE D:29 , DIO D:202BINDING SITE FOR RESIDUE DIO B 202
13BC4SOFTWARELYS B:33 , GLU B:36 , HIS B:84 , PRO B:152BINDING SITE FOR RESIDUE DIO B 203
14BC5SOFTWAREGLN B:19 , PHE B:21 , TYR D:134 , PHE D:147BINDING SITE FOR RESIDUE GOL B 204
15BC6SOFTWAREGLY C:47 , PRO C:48 , VAL C:49 , LYS C:53 , TYR C:140BINDING SITE FOR RESIDUE SO4 C 201
16BC7SOFTWAREGLY D:47 , PRO D:48 , VAL D:49 , LYS D:53 , HOH D:325BINDING SITE FOR RESIDUE SO4 D 201
17BC8SOFTWARETYR B:134 , DIO B:202 , SER D:17 , GLY D:18 , TYR D:28 , ILE D:30BINDING SITE FOR RESIDUE DIO D 202
18BC9SOFTWAREGLY D:16 , THR D:31 , SER D:64 , TYR D:67BINDING SITE FOR RESIDUE DIO D 203
19CC1SOFTWARELYS B:66 , PRO B:70 , LYS E:66 , PRO E:70 , HOH E:334BINDING SITE FOR RESIDUE SO4 E 201
20CC2SOFTWAREGLN C:105 , GLY C:106 , ARG C:107 , GLN E:136 , TRP E:138BINDING SITE FOR RESIDUE DIO E 202
21CC3SOFTWARESER E:17 , GLY E:18 , ILE E:30BINDING SITE FOR RESIDUE DIO E 203
22CC4SOFTWAREGLY F:47 , PRO F:48 , VAL F:49 , LYS F:53 , TYR F:140BINDING SITE FOR RESIDUE SO4 F 201
23CC5SOFTWARETHR E:115 , ALA F:122 , PRO F:123 , ASN F:124BINDING SITE FOR RESIDUE DIO F 202
24CC6SOFTWAREGLN C:19 , PHE C:21 , ALA F:121 , ALA F:122 , PHE F:147 , TRP F:149BINDING SITE FOR RESIDUE DIO F 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WOC)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu C:36 -Thr C:37
2Phe E:151 -Pro E:152

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WOC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WOC)

(-) Exons   (0, 0)

(no "Exon" information available for 3WOC)

(-) 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:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........eeeeee......eeeeeeee.....eeeeeeee..ee...ee....eeeeee......eeeeeeee...eeeeeeee....eeeee....eeeee.......eeeeeeeee....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3woc A  16 GSGQMFGNGKGSYFITSKDNETGITGIRVFVGPVGLIKSIQVRYGSSWSEKYGIPGGKAHELILHPGEHIISIYGRYRTFLQHVTLITNQGRSASFGLETGKGFFAAPNLTGQVLEGVYGQFWLYGITGIGFTWGFPR 153
                                    25        35        45        55        65        75        85        95       105       115       125       135       145        


Chain B from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........eeeeee......eeeeeeee.....eeeeeeee..ee...ee....eeeeee......eeeeeeee...eeeeeeee....eeee.....eeeee.......eeeeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3woc B  16 GSGQMFGNGKGSYFITSKDNETGITGIRVFVGPVGLIKSIQVRYGSSWSEKYGIPGGKAHELILHPGEHIISIYGRYRTFLQHVTLITNQGRSASFGLETGKGFFAAPNLTGQVLEGVYGQFWLYGITGIGFTWGFP 152
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       


Chain C from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...eeeeeee......eeeeeeee.....eeeeeeee..ee...ee....eeeeee......eeeeeeee...eeeeeeee....eeeee....eeeee.......eeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3woc C  16 GSGQMFGNGKGSYFITSKDNETGITGIRVFVGPVGLIKSIQVRYGSSWSEKYGIPGGKAHELILHPGEHIISIYGRYRTFLQHVTLITNQGRSASFGLETGKGFFAAPNLTGQVLEGVYGQFWLYGITGIGFTWGFP 152
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       


Chain D from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee........eeeeee......eeeeeeee.....eeeeeeee..ee...ee....eeeeee......eeeeeeee...eeeeeeee....eeee.....eeeee.......eeeeeeeee....eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3woc D  16 GSGQMFGNGKGSYFITSKDNETGITGIRVFVGPVGLIKSIQVRYGSSWSEKYGIPGGKAHELILHPGEHIISIYGRYRTFLQHVTLITNQGRSASFGLETGKGFFAAPNLTGQVLEGVYGQFWLYGITGIGFTWGFPR 153
                                    25        35        45        55        65        75        85        95       105       115       125       135       145        


Chain E from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.ee....eeeeee......eeeeeeee.....eeeeeeee..ee...ee....eeeeee......eeeeeeee...eeeeeeee....eeeee....eeeee.......eeeeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3woc E  16 GSGQMFGNGKGSYFITSKDNETGITGIRVFVGPVGLIKSIQVRYGSSWSEKYGIPGGKAHELILHPGEHIISIYGRYRTFLQHVTLITNQGRSASFGLETGKGFFAAPNLTGQVLEGVYGQFWLYGITGIGFTWGFP 152
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       


Chain F from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee........eeeeee......eeeeeeee.....eeeeeeee..ee...ee.......eee......eeeeeeee...eeeeeeee....eeee.....eeeee.......eeeeeeeee....eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3woc F  16 GSGQMFGNGKGSYFITSKDNETGITGIRVFVGPVGLIKSIQVRYGSSWSEKYGIPGGKAHELILHPGEHIISIYGRYRTFLQHVTLITNQGRSASFGLETGKGFFAAPNLTGQVLEGVYGQFWLYGITGIGFTWGFP 152
                                    25        35        45        55        65        75        85        95       105       115       125       135       145
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