Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  STREPTAVIDIN A86D MUTANT WITH LOVE-HATE LIGAND 4
 
Authors :  M. Fairhead, D. Shen, L. K. M. Chan, E. D. Lowe, T. J. Donohoe, M. Howarth
Date :  06 Feb 14  (Deposition) - 06 Aug 14  (Release) - 01 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C (2x),D (2x)
Biol. Unit 2:  A,B  (2x)
Biol. Unit 3:  C (2x),D (2x)
Keywords :  Biotin Binding Protein, Avidin, Biotin, Strain, Biotinylated, Steric Clash, Strained, Hindered, Force, Ligand Series, Affinity (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Fairhead, D. Shen, L. K. M. Chan, E. D. Lowe, T. J. Donohoe, M. Howarth
Love-Hate Ligands For High Resolution Analysis Of Strain In Ultra-Stable Protein/Small Molecule Interaction.
Bioorg. Med. Chem. V. 22 5476 2014
PubMed-ID: 25128469  |  Reference-DOI: 10.1016/J.BMC.2014.07.029

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Atcc: 27419
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: RIPL
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 37-163
    Mutation: YES
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x):   C (2x)D (2x)
Biological Unit 2 (2x): AB  
Biological Unit 3 (2x):   C (2x)D (2x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
2LH44Ligand/Ion5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4- D]IMIDAZOLIDIN-4-YL]-N'-{2,6-BIS[4-(MORPHOLINE-4- SULFONYL)PHENYL]PHENYL}PENTANEHYDRAZIDE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LH42Ligand/Ion5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4- D]IMIDAZOLIDIN-4-YL]-N'-{2,6-BIS[4-(MORPHOLINE-4- SULFONYL)PHENYL]PHENYL}PENTANEHYDRAZIDE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LH44Ligand/Ion5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4- D]IMIDAZOLIDIN-4-YL]-N'-{2,6-BIS[4-(MORPHOLINE-4- SULFONYL)PHENYL]PHENYL}PENTANEHYDRAZIDE
3PEG4Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LH42Ligand/Ion5-[(3AS,4S,6AR)-2-OXO-HEXAHYDRO-1H-THIENO[3,4- D]IMIDAZOLIDIN-4-YL]-N'-{2,6-BIS[4-(MORPHOLINE-4- SULFONYL)PHENYL]PHENYL}PENTANEHYDRAZIDE
3PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:23 , LEU A:25 , SER A:27 , TYR A:43 , SER A:45 , ALA A:46 , TYR A:54 , TRP A:79 , TYR A:83 , ARG A:84 , ASN A:85 , ASP A:86 , THR A:90 , TRP A:92 , TRP A:108 , ASP A:128 , PEG A:1136 , PEG A:1137 , HOH A:2025 , TRP B:120 , ASN C:82 , TYR C:83BINDING SITE FOR RESIDUE LH4 A1000
02AC2SOFTWAREASP A:86 , LH4 A:1000 , PEG A:1137 , CA A:1138 , TRP B:120 , LYS B:121BINDING SITE FOR RESIDUE PEG A1136
03AC3SOFTWARELH4 A:1000 , PEG A:1136 , CA A:1138 , HOH A:2092 , LYS B:121 , TYR C:83BINDING SITE FOR RESIDUE PEG A1137
04AC4SOFTWAREPEG A:1136 , PEG A:1137BINDING SITE FOR RESIDUE CA A1138
05AC5SOFTWARETRP A:120 , ASN B:23 , SER B:27 , TYR B:43 , TRP B:79 , ASP B:86 , THR B:90 , TRP B:108 , ASP B:128BINDING SITE FOR RESIDUE LH4 B1000
06AC6SOFTWAREASN C:23 , LEU C:25 , SER C:27 , TYR C:43 , SER C:45 , TRP C:79 , ASP C:86 , THR C:90 , TRP C:108 , ASP C:128 , TRP D:120BINDING SITE FOR RESIDUE LH4 C1000
07AC7SOFTWAREASN B:82 , TYR B:83 , TRP C:120 , ASN D:23 , LEU D:25 , SER D:27 , TYR D:43 , SER D:45 , ALA D:46 , TYR D:54 , TRP D:79 , TYR D:83 , ARG D:84 , ASN D:85 , ASP D:86 , THR D:90 , TRP D:108 , ASP D:128 , PEG D:1137 , HOH D:2022BINDING SITE FOR RESIDUE LH4 D1000
08AC8SOFTWAREASN B:82 , LYS C:121 , ASP D:86 , LH4 D:1000 , PEG D:1138 , CA D:1139BINDING SITE FOR RESIDUE PEG D1137
09AC9SOFTWAREASP D:86 , SER D:112 , PEG D:1137 , CA D:1139BINDING SITE FOR RESIDUE PEG D1138
10BC1SOFTWAREPEG D:1137 , PEG D:1138BINDING SITE FOR RESIDUE CA D1139

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4CPI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4CPI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4CPI)

(-) PROSITE Motifs  (1, 4)

Asymmetric 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
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 
 
 		  4-
-
C:118-132
D:118-132
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 
 
 		  4A:118-132
B:118-132
-
-
Biological Unit 3 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 
 
 		  4-
-
C:118-132
D:118-132

(-) Exons   (0, 0)

(no "Exon" information available for 4CPI)

(-) 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:119
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:119
                                    49        59        69        79        89        99       109       119       129       139       149         
            SAV_STRAV    40 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains ----------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 4cpi A  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNDHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    25        35        45        55        65        75        85        95       105       115       125         


Chain B from PDB  Type:PROTEIN  Length:118
 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 ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee....eeeeee....eeeeeee.---hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 4cpi B  15 AGITGTWYNQLGSTFIVTAGADGALTGTYES---NAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNDHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    24        34        44|   |   54        64        74        84        94       104       114       124       134 
                                                         45  49                                                                                      


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:120
                                    48        58        68        78        88        98       108       118       128       138       148       158
            SAV_STRAV    39 AGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 158
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee.....eeeeee....eeeeeee.---hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------AVIDIN_1       -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cpi C  15 AGITGTWYNQLGSTFIVTAGADGALTGTYES---NAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNDHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVK 134
                                    24        34        44|   |   54        64        74        84        94       104       114       124       134
                                                         45  49                                                                                     


Chain D 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 ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee.....eeeeee....eeeeeee....hhh.eeeeeeee..........eeeeeeeeee....eeeeeeeeeeeee.....eeeeeeeeee..hhhhhhh.eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 4cpi D  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNDHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    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  (0, 0)

(no "SCOP Domain" information available for 4CPI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4CPI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4CPI)

(-) Gene Ontology  (1, 1)

Asymmetric 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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    LH4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4cpi)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4cpi
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  SAV_STRAV | P22629
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  SAV_STRAV | P22629
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 3t6f 3t6l 3wyp 3wyq 3wzn 3wzo 3wzp 3wzq 3x00 4bx5 4bx6 4bx7 4cpe 4cpf 4cph 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

4cpe WILD-TYPE STREPTAVIDIN IN COMPLEX WITH LOVE-HATE LIGAND 1 (LH1)
4cpf WILD-TYPE STREPTAVIDIN IN COMPLEX WITH LOVE-HATE LIGAND 3 (LH3)
4cph TRANS-DIVALENT STREPTAVIDIN WITH LOVE-HATE LIGAND 4