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(-) Description

Title :  WILD-TYPE CORE STREPTAVIDIN AT ATOMIC RESOLUTION
 
Authors :  R. E. Stenkamp, Z. Wang, I. Le Trong, P. S. Stayton, T. P. Lybrand
Date :  10 May 11  (Deposition) - 24 Aug 11  (Release) - 19 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.03
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Biotin-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Le Trong, Z. Wang, D. E. Hyre, T. P. Lybrand, P. S. Stayton, R. E. Stenkamp
Streptavidin And Its Biotin Complex At Atomic Resolution.
Acta Crystallogr. , Sect. D V. 67 813 2011
PubMed-ID: 21904034  |  Reference-DOI: 10.1107/S0907444911027806

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
1MPD3Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
2MRD7Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:48 , ASN A:49 , SER A:88 , LEU A:110 , SER A:112BINDING SITE FOR RESIDUE MPD A 4002
02AC2SOFTWARETRP A:79 , THR A:90 , TRP A:92 , TRP A:108 , LEU A:110 , ASP A:128 , HOH A:6034 , HOH A:6206BINDING SITE FOR RESIDUE MRD A 4005
03AC3SOFTWAREHOH A:6098 , HOH A:6439 , TYR B:54 , ALA B:86 , SER B:88BINDING SITE FOR RESIDUE MRD B 4001
04AC4SOFTWAREHOH A:6439 , TYR B:54 , TRP B:79 , ARG B:84 , HOH B:6080BINDING SITE FOR RESIDUE MPD B 4002
05AC5SOFTWARELEU B:25 , TRP B:79 , THR B:90 , TRP B:92 , TRP B:108 , LEU B:110 , ASP B:128 , TRP C:120BINDING SITE FOR RESIDUE MRD B 4006
06AC6SOFTWARETRP B:120 , SER C:45 , TYR C:54 , TRP C:79 , ALA C:86 , SER C:88 , MRD C:4007 , HOH C:6072BINDING SITE FOR RESIDUE MRD C 4003
07AC7SOFTWARETRP B:120 , LEU C:25 , TYR C:43 , TRP C:79 , THR C:90 , TRP C:108 , LEU C:110 , ASP C:128 , MRD C:4003 , HOH C:6094 , HOH C:6209BINDING SITE FOR RESIDUE MRD C 4007
08AC8SOFTWARESER D:88 , HOH D:6111 , HOH D:6484BINDING SITE FOR RESIDUE MRD D 4004
09AC9SOFTWARETRP D:79 , THR D:90 , TRP D:92 , TRP D:108 , ASP D:128 , HOH D:6248BINDING SITE FOR RESIDUE MRD D 4008
10BC1SOFTWARETRP A:120 , ASN D:23 , TYR D:43 , TRP D:79 , THR D:90 , TRP D:92 , TRP D:108 , ASP D:128 , HOH D:6248BINDING SITE FOR RESIDUE MPD D 4009

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RY1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RY1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RY1)

(-) 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 3RY1)

(-) 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: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 d3ry1a_ A: Streptavidin                                                                                                    SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       ---- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ry1 A  15 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPS 136
                                    24        34        44        54        64        74        84        94       104       114       124       134  


Chain B from PDB  Type:PROTEIN  Length:126
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:126
                                    47        57        67        77        87        97       107       117       127       137       147       157      
            SAV_STRAV    38 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAAS 163
               SCOP domains d3ry1b_ B: Streptavidin                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeee....eeeeeee....eeeeeeee...hhhhheeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------AVIDIN_1       ------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ry1 B  14 EAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPSAAS 139
                                    23        33        43        53        63        73        83        93       103       113       123       133      


Chain C from PDB  Type:PROTEIN  Length:121
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:121
                                    48        58        68        78        88        98       108       118       128       138       148       158 
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d3ry1c_ C: Streptavidin                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.....eeeeee....eeeeeee........eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ry1 C  15 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    24        34        44        54        64        74        84        94       104       114       124       134 


Chain D from PDB  Type:PROTEIN  Length:121
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:121
                                    49        59        69        79        89        99       109       119       129       139       149       159 
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPS 160
               SCOP domains d3ry1d_ D: Streptavidin                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee....hhhhheeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee.....hhhh.eeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ry1 D  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKPS 136
                                    25        35        45        55        65        75        85        95       105       115       125       135
   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  (0, 0)

(no "CATH Domain" information available for 3RY1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3RY1)

(-) 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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  3ry1
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  SAV_STRAV | P22629
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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 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

3ry2