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(-) Description

Title :  STREPTAVIDIN MUTANT Y43F
 
Authors :  S. Freitag, I. Le Trong, L. A. Klumb, P. S. Stayton, R. E. Stenkamp
Date :  12 Oct 98  (Deposition) - 10 Nov 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.14
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Biotin Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Freitag, I. Le Trong, L. A. Klumb, P. S. Stayton, R. E. Stenkamp
Atomic Resolution Structure Of Biotin-Free Tyr43Phe Streptavidin: What Is In The Binding Site?
Acta Crystallogr. , Sect. D V. 55 1118 1999
PubMed-ID: 10329773  |  Reference-DOI: 10.1107/S0907444999002322
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: T7 EXPRESSION SYSTEM
    Expression System Plasmid: PET-210 , NOVAGEN, INC., MADISON,WI
    Expression System Taxid: 562
    Mutation: YES
    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  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1MPD5Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD1Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:25 , TRP A:79 , THR A:90 , TRP A:92 , TRP A:108 , ASP A:128 , HOH A:520BINDING SITE FOR RESIDUE MRD A 1
2AC2SOFTWAREGLY A:48 , ASN A:49 , SER A:88 , SER A:112 , HOH A:491 , TRP D:120BINDING SITE FOR RESIDUE MPD A 2
3AC3SOFTWARETHR B:90 , TRP B:92 , TRP B:108 , LEU B:110 , ASP B:128BINDING SITE FOR RESIDUE MPD B 3
4AC4SOFTWARETHR C:90 , TRP C:92 , TRP C:108 , LEU C:110 , ASP C:128BINDING SITE FOR RESIDUE MPD C 4
5AC5SOFTWARETRP C:79 , SER C:88BINDING SITE FOR RESIDUE MPD C 5
6AC6SOFTWARETRP A:120 , ASN D:23 , TRP D:79 , THR D:90 , TRP D:92 , TRP D:108 , LEU D:110 , ASP D:128BINDING SITE FOR RESIDUE MPD D 6

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1SWU)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric/Biological Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 
 
 		  4A:118-132
B:118-132
C:118-132
D:118-132

(-) Exons   (0, 0)

(no "Exon" information available for 1SWU)

(-) 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
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:120
                                    49        59        69        79        89        99       109       119       129       139       149       159
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d1swua_ A: Streptavidin                                                                                                  SCOP domains
               CATH domains 1swuA00 A:16-135  [code=2.40.128.30, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee........eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1swu A  16 GITGTWYNQLGSTFIVTAGADGALTGTFESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    25        35        45        55        65        75        85        95       105       115       125       135


Chain B from PDB  Type:PROTEIN  Length:116
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:119
                                    48        58        68        78        88        98       108       118       128       138       148         
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1swub_ B: Streptavidin                                                                                                 SCOP domains
               CATH domains 1swuB00 B:15-133  [code=2.40.12   8.30, no name defined]                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeeeee....eeeeeee.---.hhh.eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1swu B  15 AGITGTWYNQLGSTFIVTAGADGALTGTFES---NAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    24        34        44|   |   54        64        74        84        94       104       114       124         
                                                         45  49                                                                                    


Chain C from PDB  Type:PROTEIN  Length:114
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1swuc_ C: Streptavidin                                                                                                SCOP domains
               CATH domains 1swuC00 C:16-133  [code=2.40.12    8.30, no name defined]                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee..----..eeeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1swu C  16 GITGTWYNQLGSTFIVTAGADGALTGTFESA----ESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        45|    |  55        65        75        85        95       105       115       125        
                                                         46   51                                                                                  


Chain D from PDB  Type:PROTEIN  Length:115
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:118
                                    49        59        69        79        89        99       109       119       129       139       149        
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d1swud_ D: Streptavidin                                                                                                SCOP domains
               CATH domains 1swuD00 D:16-133  [code=2.40.   128.30, no name defined]                                                               CATH domains
           Pfam domains (1) Avidin-1swuD01 D:16-132                                                                                              - Pfam domains (1)
           Pfam domains (2) Avidin-1swuD02 D:16-132                                                                                              - Pfam domains (2)
           Pfam domains (3) Avidin-1swuD03 D:16-132                                                                                              - Pfam domains (3)
           Pfam domains (4) Avidin-1swuD04 D:16-132                                                                                              - Pfam domains (4)
         Sec.struct. author ...eeee.....eeeeee....eeeeeee---..hhh.eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 1swu D  16 GITGTWYNQLGSTFIVTAGADGALTGTFE---GNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    25        35        |-  |     55        65        75        85        95       105       115       125        
                                                       44  48
   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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Avidin] (113)
(-)
Family: Avidin (113)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (SAV_STRAV | P22629)
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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  1swu
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        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 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 3wyp 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

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