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(-) Description

Title :  CRYSTAL STRUCTURE OF WILD-TYPE CORE STREPTAVIDIN IN COMPLEX WITH D-BIOTIN/BIOTIN-D-SULFOXIDE AT 1.3 A RESOLUTION
 
Authors :  T. Kawato, E. Mizohata, T. Meshizuka, H. Doi, T. Kawamura, H. Matsumura K. Yumura, K. Tsumoto, T. Kodama, T. Inoue, A. Sugiyama
Date :  05 Sep 14  (Deposition) - 24 Dec 14  (Release) - 24 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Beta-Barrel, Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kawato, E. Mizohata, T. Meshizuka, H. Doi, T. Kawamura, H. Matsumura, K. Yumura, K. Tsumoto, T. Kodama, T. Inoue, A. Sugiyama
Crystal Structure Of Streptavidin Mutant With Low Immunogenicity
J. Biosci. Bioeng. 2014
PubMed-ID: 25434833  |  Reference-DOI: 10.1016/J.JBIOSC.2014.10.025

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A, B, D, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PPAL7
    Expression System Strain: BL21STAR(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 37-163
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1BSO2Ligand/IonBIOTIN-D-SULFOXIDE
2BTN2Ligand/IonBIOTIN
3GOL10Ligand/IonGLYCEROL
4SO42Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:23 , LEU A:25 , SER A:27 , TYR A:43 , SER A:45 , VAL A:47 , GLY A:48 , ASN A:49 , TRP A:79 , SER A:88 , THR A:90 , TRP A:108 , ASP A:128 , HOH A:1170 , TRP D:120 , GOL D:1002BINDING SITE FOR RESIDUE BTN A 1001
02AC2SOFTWAREGLN A:24 , LEU A:25 , GLY A:126 , HIS A:127 , GOL A:1004 , HOH A:1123 , HOH A:1145 , HOH A:1163BINDING SITE FOR RESIDUE GOL A 1002
03AC3SOFTWAREGLY A:26 , SER A:27 , THR A:28 , GLU A:44 , ALA A:46BINDING SITE FOR RESIDUE GOL A 1003
04AC4SOFTWAREHIS A:127 , GOL A:1002 , HOH A:1189 , HOH A:1203 , HOH A:1213 , THR C:129 , HOH C:1119BINDING SITE FOR RESIDUE GOL A 1004
05AC5SOFTWAREASN B:23 , LEU B:25 , SER B:27 , TYR B:43 , SER B:45 , VAL B:47 , ASN B:49 , TRP B:79 , SER B:88 , THR B:90 , TRP B:108 , LEU B:110 , ASP B:128 , HOH B:1147 , HOH B:1212 , TRP C:120BINDING SITE FOR RESIDUE BSO B 1001
06AC6SOFTWAREGLN B:24 , LEU B:25 , GLY B:126 , HIS B:127 , HOH B:1124 , HOH B:1132BINDING SITE FOR RESIDUE GOL B 1002
07AC7SOFTWAREGLY B:26 , SER B:27 , THR B:28 , GLU B:44BINDING SITE FOR RESIDUE GOL B 1003
08AC8SOFTWAREHIS A:87 , ALA B:65 , THR B:66 , HOH B:1167 , HOH B:1168 , HOH B:1211BINDING SITE FOR RESIDUE SO4 B 1004
09AC9SOFTWARETRP A:120 , ASN D:23 , LEU D:25 , SER D:27 , TYR D:43 , SER D:45 , VAL D:47 , GLY D:48 , ASN D:49 , TRP D:79 , SER D:88 , THR D:90 , TRP D:108 , ASP D:128 , HOH D:1127 , HOH D:1224BINDING SITE FOR RESIDUE BTN D 1001
10BC1SOFTWAREBTN A:1001 , HOH A:1170 , HOH D:1139 , HOH D:1170BINDING SITE FOR RESIDUE GOL D 1002
11BC2SOFTWAREGLN D:24 , LEU D:25 , GLY D:126 , HIS D:127 , HOH D:1121 , HOH D:1148 , HOH D:1174 , HOH D:1202 , HOH D:1222BINDING SITE FOR RESIDUE GOL D 1003
12BC3SOFTWAREASP C:36 , ARG C:59 , SER C:62 , HOH C:1115 , LYS D:80 , ASN D:81 , ASN D:82BINDING SITE FOR RESIDUE GOL D 1004
13BC4SOFTWARETRP B:120 , ASN C:23 , LEU C:25 , SER C:27 , TYR C:43 , SER C:45 , VAL C:47 , ASN C:49 , TRP C:79 , SER C:88 , THR C:90 , TRP C:108 , LEU C:110 , ASP C:128 , GOL C:1003BINDING SITE FOR RESIDUE BSO C 1001
14BC5SOFTWARETRP B:120 , GLN C:24 , LEU C:25 , GLY C:126 , HIS C:127 , HOH C:1125BINDING SITE FOR RESIDUE GOL C 1002
15BC6SOFTWARESER C:112 , BSO C:1001 , HOH C:1134BINDING SITE FOR RESIDUE GOL C 1003
16BC7SOFTWAREGLY B:48 , HOH B:1148 , HOH B:1164 , ALA C:65 , THR C:66 , ASP C:67 , LYS C:121 , HOH C:1137 , HOH C:1143 , HOH C:1178 , HOH C:1199BINDING SITE FOR RESIDUE SO4 C 1004

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:15 -Gly A:16
2Glu D:14 -Ala D:15
3Ala D:100 -Glu D:101

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3WYP)

(-) Sequences/Alignments

Asymmetric/Biological 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:120
                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3wyp A  15 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    24        34        44        54        64        74        84        94       104       114       124       134


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee.....hhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyp B  14 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    23        33        43        53        63        73        83        93       103       113       123       133  


Chain C from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyp C  13 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    22        32        42        52        62        72        82        92       102       112       122       132  


Chain D from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee.....hhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wyp D  14 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    23        33        43        53        63        73        83        93       103       113       123       133
   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  (0, 0)

(no "SCOP Domain" information available for 3WYP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WYP)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WYP)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:15 - Gly A:16   [ RasMol ]  
    Ala D:100 - Glu D:101   [ RasMol ]  
    Glu D:14 - Ala D:15   [ RasMol ]  
 

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        SAV_STRAV | P22629: 1df8 1hqq 1hxl 1hxz 1hy2 1i9h 1kff 1kl3 1kl4 1kl5 1lcv 1lcw 1lcz 1luq 1mep 1mk5 1mm9 1moy 1n43 1n4j 1n7y 1n9m 1n9y 1nbx 1nc9 1ndj 1nqm 1pts 1rst 1rsu 1rxh 1rxj 1rxk 1sld 1sle 1slf 1slg 1sre 1srf 1srg 1srh 1sri 1srj 1stp 1str 1sts 1swa 1swb 1swc 1swd 1swe 1swf 1swg 1swh 1swj 1swk 1swl 1swn 1swo 1swp 1swq 1swr 1sws 1swt 1swu 1vwa 1vwb 1vwc 1vwd 1vwe 1vwf 1vwg 1vwh 1vwi 1vwj 1vwk 1vwl 1vwm 1vwn 1vwo 1vwp 1vwq 1vwr 2bc3 2f01 2g5l 2gh7 2iza 2izb 2izc 2izd 2ize 2izf 2izg 2izh 2izi 2izj 2izk 2izl 2qcb 2rta 2rtb 2rtc 2rtd 2rte 2rtf 2rtg 2rth 2rti 2rtj 2rtk 2rtl 2rtm 2rtn 2rto 2rtp 2rtq 2rtr 2wpu 2y3e 2y3f 3mg5 3pk2 3rdm 3rdo 3rdq 3rds 3rdu 3rdx 3re5 3re6 3ry1 3ry2 3t6f 3t6l 3wyq 3wzn 3wzo 3wzp 3wzq 3x00 4bx5 4bx6 4bx7 4cpe 4cpf 4cph 4cpi 4dne 4ekv 4gd9 4gda 4gjs 4gjv 4irw 4jo6 4oka 4y59 4y5d 4yvb 5b5f 5b5g 5cse 5f2b 5jd2 5k49 5k67 5k68 5l3y 5to2

(-) Related Entries Specified in the PDB File

3wyq