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(-) Description

Title :  STRUCTURE OF SAVM-W120K, STREPTAVIDIN MUTANT
 
Authors :  Y. Pazy, Y. Eisenberg-Domovich, O. H. Laitinen, M. S. Kulomaa, E. A. Bayer, M. Wilchek, O. Livnah
Date :  22 Jan 03  (Deposition) - 15 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Avidin, Streptavidin, Biotin, Monomer-Monomer Interaction, High Affinity Systems, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Pazy, Y. Eisenberg-Domovich, O. H. Laitinen, M. S. Kulomaa, E. A. Bayer, M. Wilchek, O. Livnah
Dimer-Tetramer Transition Between Solution And Crystalline States Of Streptavidin And Avidin Mutants.
J. Bacteriol. V. 185 4050 2003
PubMed-ID: 12837778  |  Reference-DOI: 10.1128/JB.185.14.4050-4056.2003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: JM109
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    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  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1BTN4Ligand/IonBIOTIN

(-) 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 , ASP A:128 , HOH A:978 , LYS B:320BINDING SITE FOR RESIDUE BTN A 150
2AC2SOFTWARELYS A:120 , ASN B:223 , SER B:227 , TYR B:243 , SER B:245 , VAL B:247 , ASN B:249 , TRP B:279 , SER B:288 , THR B:290 , TRP B:308 , ASP B:328 , HOH B:887BINDING SITE FOR RESIDUE BTN B 350
3AC3SOFTWAREASN C:423 , SER C:427 , TYR C:443 , SER C:445 , VAL C:447 , ASN C:449 , TRP C:479 , SER C:488 , THR C:490 , TRP C:508 , ASP C:528 , HOH C:977 , LYS D:720BINDING SITE FOR RESIDUE BTN C 550
4AC4SOFTWARELYS C:520 , ASN D:623 , SER D:627 , TYR D:643 , SER D:645 , VAL D:647 , ASN D:649 , TRP D:679 , SER D:688 , THR D:690 , TRP D:708 , ASP D:728 , HOH D:979BINDING SITE FOR RESIDUE BTN D 750

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) 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:318-332
C:518-532
D:718-732

(-) Exons   (0, 0)

(no "Exon" information available for 1NQM)

(-) 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:118
 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 d1nqma_ A: Streptavidin                                                                                                SCOP domains
               CATH domains 1nqmA00 A:16-133  [code=2.40.128.30, no name defined]                                                                  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
                 1nqm A  16 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAKKSTLVGHDTFTKV 133
                                    25        35        45        55        65        75        85        95       105       115       125        


Chain B 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 d1nqmb_ B: Streptavidin                                                                                                 SCOP domains
               CATH domains 1nqmB00 B:216-334  [code=2.40.128.30, no name defined]                                                                  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
                 1nqm B 216 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAKKSTLVGHDTFTKVK 334
                                   225       235       245       255       265       275       285       295       305       315       325         


Chain C 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 d1nqmc_ C: Streptavidin                                                                                                 SCOP domains
               CATH domains 1nqmC00 C:416-534  [code=2.40.128.30, no name defined]                                                                  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
                 1nqm C 416 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAKKSTLVGHDTFTKVK 534
                                   425       435       445       455       465       475       485       495       505       515       525         


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 d1nqmd_ D: Streptavidin                                                                                                  SCOP domains
               CATH domains 1nqmD00 D:616-735  [code=2.40.128.30, no name defined]                                                                   CATH domains
           Pfam domains (1) Avidin-1nqmD01 D:616-732                                                                                             --- Pfam domains (1)
           Pfam domains (2) Avidin-1nqmD02 D:616-732                                                                                             --- Pfam domains (2)
           Pfam domains (3) Avidin-1nqmD03 D:616-732                                                                                             --- Pfam domains (3)
           Pfam domains (4) Avidin-1nqmD04 D:616-732                                                                                             --- Pfam domains (4)
         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
                 1nqm D 616 GITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAKKSTLVGHDTFTKVKP 735
                                   625       635       645       655       665       675       685       695       705       715       725       735
   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)
(-)
Streptomyces avidinii (97)
1aAvidin-1nqmD01D:616-732
1bAvidin-1nqmD02D:616-732
1cAvidin-1nqmD03D:616-732
1dAvidin-1nqmD04D:616-732

(-) 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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 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 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 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

(no "Related Entries Specified in the PDB File" available for 1NQM)