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(-) Description

Title :  TRAPTAVIDIN, BIOTIN BOUND FORM
 
Authors :  C. E. Chivers, A. L. Koner, E. D. Lowe, M. Howarth
Date :  20 Dec 10  (Deposition) - 16 Feb 11  (Release) - 06 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.49
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Biotin-Binding Protein, Protein Engineering (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. E. Chivers, A. L. Koner, E. D. Lowe, M. Howarth
How The Biotin-Streptavidin Interaction Was Made Even Stronger: Investigation Via Crystallography And A Chimeric Tetramer.
Biochem. J. V. 435 55 2011
PubMed-ID: 21241253  |  Reference-DOI: 10.1042/BJ20101593

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: RIPL
    Expression System Taxid: 562
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 37-163
    Mutation: YES
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895
    Other Details: STREPTAVIDIN MUTATED TO INCREASE BIOTIN BINDING AFFINITY
    Synonym: TRAPTAVIDIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1BTN1Ligand/IonBIOTIN
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1BTN4Ligand/IonBIOTIN
2GOL12Ligand/IonGLYCEROL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN 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 , LEU A:110 , TRP A:120 , ASP A:128 , GOL A:1137BINDING SITE FOR RESIDUE BTN A1136
2AC2SOFTWARELEU A:110 , SER A:112 , BTN A:1136 , HOH A:2121 , HOH A:2122BINDING SITE FOR RESIDUE GOL A1137
3AC3SOFTWARESER A:93 , GLY A:94 , GLN A:95 , ASN A:105 , THR A:106 , GLN A:107 , THR A:111 , SER A:122 , THR A:123BINDING SITE FOR RESIDUE GOL A1138
4AC4SOFTWAREASP A:53 , ASP A:67 , ASN A:81 , ASN A:82 , TYR A:83 , HOH A:2124BINDING SITE FOR RESIDUE GOL A1139

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y3F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3F)

(-) PROSITE Motifs  (1, 1)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3F)

(-) 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
                                    48        58        68        78        88        98       108       118       128       138       148       158 
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d2y3fa_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Avidin-2y3fA01 A:15-132                                                                                               --- 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
                 2y3f A  15 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAEGDYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    24        34        44        54        64        74        84        94       104       114       124       134
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3F)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (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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  2y3f
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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 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

1df8 S45A MUTANT OF STREPTAVIDIN IN COMPLEX WITH BIOTIN
1hqq MINIPROTEIN MP-2 (M9A) COMPLEX WITH STREPTAVIDIN
1hxl MINIPROTEIN MP-2 (V10A) COMPLEX WITH STREPTAVIDIN
1hxz MINIPROTEIN MP-2 COMPLEX WITH STREPTAVIDIN
1hy2 MINIPROTEIN MP-1 COMPLEX WITH STREPTAVIDIN
1i9h CORE STREPTAVIDIN-BNA COMPLEX
1kff AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THESTREP-TAG II PEPTIDE: APO-SAM1
1kl3 AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THESTREP-TAG II PEPTIDE : SAM1-STREPII
1kl4 AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THESTREP-TAG II PEPTIDE : APO-SAM2
1kl5 AN ENGINEERED STREPTAVIDIN WITH IMPROVED AFFINITY FOR THESTREP-TAG II PEPTIDE : SAM2-STREPII
1lcv STREPTAVIDIN-NORBIOTIN COMPLEX
1lcw STREPTAVIDIN-HOMOBIOTIN COMPLEX
1lcz STREPTAVIDIN-BCAP COMPLEX
1luq FULL MATRIX ERROR ANALYSIS OF STREPTAVIDIN
1mep CRYSTAL STRUCTURE OF STREPTAVIDIN DOUBLE MUTANT S45A/ D128AWITH BIOTIN: COOPERATIVE HYDROGEN-BOND INTERACTIONS IN THESTREPTAVIDIN-BIOTIN SYSTEM.
1mk5 WILDTYPE CORE-STREPTAVIDIN WITH BIOTIN AT 1.4A.
1mm9 STREPTAVIDIN MUTANT WITH INSERTION OF FIBRONECTINHEXAPEPTIDE , INCLUDING RGD
1moy STREPTAVIDIN MUTANT WITH OSTEOPONTIN HEXAPEPTIDE INSERTIONINCLUDING RGD
1n43 STREPTAVIDIN MUTANT N23A WITH BIOTIN AT 1.89A
1n4j STREPTAVIDIN MUTANT N23A AT 2.18A
1n7y STREPTAVIDIN MUTANT N23E AT 1.96A
1n9m STREPTAVIDIN MUTANT S27A WITH BIOTIN AT 1.6A RESOLUTION
1n9y STREPTAVIDIN MUTANT S27A AT 1.5A RESOLUTION
1nbx STREPTAVIDIN MUTANT Y43A AT 1.70A RESOLUTION
1nc9 STREPTAVIDIN MUTANT Y43A WITH IMINOBIOTIN AT 1.8A RESOLUTION
1ndj STREPTAVIDIN MUTANT Y43F WITH BIOTIN AT 1.81A RESOLUTION
1nqm STRUCTURE OF SAVM-W120K, STREPTAVIDIN MUTANT
1pts STREPTAVIDIN COMPLEX WITH THE PEPTIDE (FSHPQNT)
1rst COMPLEX BETWEEN STREPTAVIDIN AND THE STREP-TAG PEPTIDE
1rsu COMPLEX BETWEEN STREPTAVIDIN AND THE STREP-TAG II PEPTIDE
1rxh CRYSTAL STRUCTURE OF STREPTAVIDIN MUTANT L124R (M1) COMPLEXED WITH BIOTINYL P-NITROANILIDE (BNI)
1rxj CRYSTAL STRUCTURE OF STREPTAVIDIN MUTANT (M2) WHERE THE L3,4 LOOP WAS REPLACE BY THAT OF AVIDIN
1rxk CRYSTAL STRUCTURE OF STREPTAVIDIN MUTANT (M3) A COMBINATIONOF M1+M2
1sld STREPTAVIDIN, PH 7.5, BOUND TO CYCLIC DISULFIDE-BONDED PEPTIDE LIGAND AC-CHPQFC-NH2
1sle STREPTAVIDIN, PH 5.0, BOUND TO CYCLIC PEPTIDE AC- CHPQGPPC-NH2
1slf APOSTREPTAVIDIN, PH 5.6, TWO MOLECULES OF (SO4)2 BOUND AT THE BIOTIN BINDING SITE
1slg STREPTAVIDIN, PH 5.6, BOUND TO PEPTIDE FCHPQNT
1sre STREPTAVIDIN COMPLEXED WITH HABA
1srf STREPTAVIDIN COMPLEXED WITH 3'-TERT-BUTYL-HABA
1srg STREPTAVIDIN COMPLEXED WITH 3'-METHYL-HABA
1srh STREPTAVIDIN COMPLEXED WITH 3',5'-DIMETHOXY-HABA
1sri STREPTAVIDIN COMPLEXED WITH 3',5'-DIMETHYL-HABA
1srj STREPTAVIDIN COMPLEXED WITH NAPHTHYL-HABA
1stp STREPTAVIDIN COMPLEX WITH BIOTIN
1str STREPTAVIDIN DIMERIZED BY DISULFIDE-BONDED PEPTIDE AC- CHPQNT-NH2 DIMER
1sts STREPTAVIDIN DIMERIZED BY DISULFIDE-BONDED PEPTIDE FCHPQNT -NH2 DIMER
1swa APO-CORE-STREPTAVIDIN AT PH 4.5
1swb APO-CORE-STREPTAVIDIN AT PH 7.5
1swc APO-CORE-STREPTAVIDIN AT PH 4.5
1swd APO-CORE-STREPTAVIDIN IN COMPLEX WITH BIOTIN (TWO UNOCCUPIED BINDING SITES) AT PH 4.5
1swe APO-CORE-STREPTAVIDIN IN COMPLEX WITH BIOTIN AT PH 4.5
1swf CIRCULAR PERMUTED STREPTAVIDIN E51/A46
1swg CIRCULAR PERMUTED STREPTAVIDIN E51/A46 IN COMPLEX WITH BIOTIN
1swh CORE-STREPTAVIDIN MUTANT W79F AT PH 4.5
1swj CORE-STREPTAVIDIN MUTANT W79F AT PH 4.5
1swk CORE-STREPTAVIDIN MUTANT W79F IN COMPLEX WITH BIOTIN AT PH 4.5
1swl CORE-STREPTAVIDIN MUTANT W108F AT PH 7.0
1swn CORE-STREPTAVIDIN MUTANT W108F IN COMPLEX WITH BIOTIN AT PH 7.0
1swo CORE-STREPTAVIDIN MUTANT W120F AT PH 7.5
1swp CORE-STREPTAVIDIN MUTANT W120F IN COMPLEX WITH BIOTIN AT PH 7.5
1swq CORE-STREPTAVIDIN MUTANT W120A AT PH 7.5
1swr CORE-STREPTAVIDIN MUTANT W120A IN COMPLEX WITH BIOTIN AT PH 7.5
1sws CORE-STREPTAVIDIN MUTANT D128A AT PH 4.5
1swt CORE-STREPTAVIDIN MUTANT D128A IN COMPLEX WITH BIOTIN AT PH 4.5
1swu STREPTAVIDIN MUTANT Y43F
1vwa STREPTAVIDIN-FSHPQNT
1vwb STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 11.8
1vwc STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 2.0
1vwd STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.0
1vwe STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 3.6
1vwf STREPTAVIDIN COMPLEXED WITH CYCLO-AC-[CHPQGPPC]-NH2 MONOMER, PH 3.67
1vwg STREPTAVIDIN COMPLEXED WITH THE HEAD-TO-TAIL DISULFIDE- BONDED PEPTIDE DIMER OF CYCLO-AC-[CHPQGPPC]-NH2, PH 2.5
1vwh STREPTAVIDIN COMPLEXED WITH THE HEAD-TO-TAIL DISULFIDE- BONDED PEPTIDE DIMER OF CYCLO-AC-[CHPQGPPC]-NH2, PH 3.5
1vwi STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 1.5, I222 COMPLEX
1vwj STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 2.5, I222 COMPLEX
1vwk STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2
1vwl STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 3.5, I222 COMPLEX
1vwm STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 4.2
1vwn STREPTAVIDIN-CYCLO-AC-[CHPQFC]-NH2, PH 4.8
1vwo STREPTAVIDIN COMPLEXED WITH CYCLO-AC-[CHPQGPPC]-NH2 MONOMER, PH 2.85
1vwp STREPTAVIDIN COMPLEXED WITH CYCLO-AC-[CHPQGPPC]-NH2 MONOMER, PH 2.5
1vwq STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 2.5, I4122 COMPLEX
1vwr STREPTAVIDIN-CYCLO-[5-S-VALERAMIDE-HPQGPPC]K-NH2, PH 3.5, I4122 COMPLEX
2bc3 T7-TAGGED FULL-LENGTH STREPTAVIDIN
2f01 EPI-BIOTIN COMPLEX WITH CORE STREPTAVIDIN
2iza APOSTREPTAVIDIN PH 2.00 I4122 STRUCTURE
2izb APOSTREPTAVIDIN PH 3.12 I4122 STRUCTURE
2izc APOSTREPTAVIDIN PH 2.0 I222 COMPLEX
2izd APOSTREPTAVIDIN PH 3.0 I222 COMPLEX
2ize APOSTREPTAVIDIN PH 3.08 I222 COMPLEX
2izf STREPTAVIDIN-BIOTIN PH 4.0 I222 COMPLEX
2izg STREPTAVIDIN-BIOTIN PH 2.0 I222 COMPLEX
2izh STREPTAVIDIN-BIOTIN PH 10.44 I222 COMPLEX
2izi STREPTAVIDIN-BIOTIN PH 2.53 I4122 STRUCTURE
2izj STREPTAVIDIN-BIOTIN PH 3.50 I4122 STRUCTURE
2izk STREPTAVIDIN-GLYCOLURIL PH 2.58 I4122 COMPLEX
2izl STREPTAVIDIN-2-IMINOBIOTIN PH 7.3 I222 COMPLEX
2rta APOSTREPTAVIDIN, PH 2.97, SPACE GROUP I4122
2rtb APOSTREPTAVIDIN, PH 3.32, SPACE GROUP I222
2rtc APOSTREPTAVIDIN, PH 3.60, SPACE GROUP I222
2rtd STREPTAVIDIN-BIOTIN COMPLEX, PH 1.39, SPACE GROUP I222
2rte STREPTAVIDIN-BIOTIN COMPLEX, PH 1.90, SPACE GROUP I222
2rtf STREPTAVIDIN-BIOTIN COMPLEX, PH 2.00, SPACE GROUP I222
2rtg STREPTAVIDIN-BIOTIN COMPLEX, PH 2.40, SPACE GROUP I222
2rth STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I222
2rti STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I222
2rtj STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I4122
2rtk STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.58, SPACE GROUP I4122 PREPARED FROM AN APOSTREPTAVIDIN CRYSTAL
2rtl STREPTAVIDIN-2-IMINOBIOTIN-SULFATE COMPLEX, PH 2.50, SPACE GROUP I4122
2rtm STREPTAVIDIN-2-IMINOBIOTIN-SULFATE COMPLEX, PH 3.50, SPACE GROUP I4122
2rtn STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 2.0, SPACE GROUP I222
2rto STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 2.6, SPACE GROUP I222
2rtp STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 3.25, SPACE GROUP I222
2rtq STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 3.25, SPACE GROUP I222, CRYSTALLIZED FROM 4.3 M AMMONIUM SULFATE
2rtr STREPTAVIDIN-2-IMINOBIOTIN COMPLEX, PH 4.0, SPACE GROUP I222
2wpu CHAPERONED RUTHENIUM METALLODRUGS THAT RECOGNIZE TELOMERIC DNA
2y3e TRAPTAVIDIN, APO-FORM