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(-) Description

Title :  BIOTIN COMPLEX OF Y54F CORE STREPTAVIDIN
 
Authors :  L. Baugh, I. Le Trong, D. S. Cerutti, N. Mehta, S. Gulich, P. S. Stayton, R. E. Stenkamp, T. P. Lybrand
Date :  28 Jul 11  (Deposition) - 21 Dec 11  (Release) - 08 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.22
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Biotin Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Baugh, I. Le Trong, D. S. Cerutti, N. Mehta, S. Gulich, P. S. Stayton R. E. Stenkamp, T. P. Lybrand
Second-Contact Shell Mutation Diminishes Streptavidin-Bioti Binding Affinity Through Transmitted Effects On Equilibrium Dynamics.
Biochemistry V. 51 597 2012
PubMed-ID: 22145986  |  Reference-DOI: 10.1021/BI201221J

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 37-163
    Mutation: YES
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1BSO2Ligand/IonBIOTIN-D-SULFOXIDE
2BTN2Ligand/IonBIOTIN
3GOL4Ligand/IonGLYCEROL
4SO43Ligand/IonSULFATE ION
Biological Unit 1 (3, 18)
No.NameCountTypeFull Name
1BSO4Ligand/IonBIOTIN-D-SULFOXIDE
2BTN-1Ligand/IonBIOTIN
3GOL8Ligand/IonGLYCEROL
4SO46Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:23 , LEU A:25 , SER A:27 , TYR A:43 , SER A:45 , VAL A:47 , ASN A:49 , TRP A:79 , SER A:88 , THR A:90 , TRP A:108 , ASP A:128 , BSO A:5101 , HOH A:6145 , HOH A:6170BINDING SITE FOR RESIDUE BTN A 5100
02AC2SOFTWAREASN A:23 , LEU A:25 , SER A:27 , TYR A:43 , SER A:45 , VAL A:47 , ASN A:49 , TRP A:79 , SER A:88 , THR A:90 , TRP A:108 , LEU A:110 , ASP A:128 , BTN A:5100 , HOH A:6145 , HOH A:6170BINDING SITE FOR RESIDUE BSO A 5101
03AC3SOFTWAREHOH A:6223 , HOH A:6224 , BTN B:5200 , BSO B:5201 , HOH B:6158BINDING SITE FOR RESIDUE GOL A 5400
04AC4SOFTWAREVAL A:47 , GLY A:48 , HOH A:6171 , LYS B:121 , GOL B:5402 , HOH B:6142BINDING SITE FOR RESIDUE GOL A 5403
05AC5SOFTWARETRP A:120 , GOL A:5400 , ASN B:23 , LEU B:25 , SER B:27 , TYR B:43 , SER B:45 , VAL B:47 , ASN B:49 , TRP B:79 , ALA B:86 , SER B:88 , THR B:90 , TRP B:108 , ASP B:128 , BSO B:5201 , HOH B:6158BINDING SITE FOR RESIDUE BTN B 5200
06AC6SOFTWARETRP A:120 , GOL A:5400 , ASN B:23 , LEU B:25 , SER B:27 , TYR B:43 , SER B:45 , VAL B:47 , ASN B:49 , TRP B:79 , ALA B:86 , SER B:88 , THR B:90 , TRP B:108 , LEU B:110 , ASP B:128 , BTN B:5200 , HOH B:6158BINDING SITE FOR RESIDUE BSO B 5201
07AC7SOFTWAREGLY B:34 , ALA B:35 , ASP B:36 , GLY B:37 , ALA B:38 , HOH B:6156 , HOH B:6218BINDING SITE FOR RESIDUE SO4 B 5300
08AC8SOFTWAREASN A:82 , TYR A:83 , HOH A:6070 , THR B:42 , ARG B:53BINDING SITE FOR RESIDUE SO4 B 5301
09AC9SOFTWAREGLY B:99 , ALA B:100 , VAL B:133 , LYS B:134 , HOH B:6101BINDING SITE FOR RESIDUE SO4 B 5302
10BC1SOFTWAREGLY A:48 , ASN A:49 , GOL A:5403 , HOH A:6170 , LYS B:121 , HOH B:6142BINDING SITE FOR RESIDUE GOL B 5402
11BC2SOFTWARETHR A:115 , GLU B:51 , ASP B:67 , TYR B:83BINDING SITE FOR RESIDUE GOL B 5404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3T6F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3T6F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3T6F)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 		  2A:118-132
B:118-132
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 		  4A:118-132
B:118-132

(-) Exons   (0, 0)

(no "Exon" information available for 3T6F)

(-) 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:121
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:121
                                    47        57        67        77        87        97       107       117       127       137       147       157 
            SAV_STRAV    38 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains d3t6fa_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t6f A  14 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRFVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    23        33        43        53        63        73        83        93       103       113       123       133 


Chain B from PDB  Type:PROTEIN  Length:122
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:122
                                    48        58        68        78        88        98       108       118       128       138       148       158  
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPS 160
               SCOP domains d3t6fb_ B: automated matches                                                                                               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 -------------------------------------------------------------------------------------------------------AVIDIN_1       ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3t6f B  15 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRFVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPS 136
                                    24        34        44        54        64        74        84        94       104       114       124       134
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  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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3T6F)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3T6F)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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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  3t6f
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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 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 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

3t6l