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(-) Description

Title :  STREPTAVIDIN-GLYCOLURIL COMPLEX, PH 2.50, SPACE GROUP I222
 
Authors :  B. A. Katz
Date :  11 Sep 97  (Deposition) - 14 Oct 98  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  B,D
Biol. Unit 1:  B,D  (2x)
Biol. Unit 2:  B,D  (4x)
Keywords :  Biotin-Binding Protein, Streptavidin-Glycoluril, Ph 2. 50 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. A. Katz
Binding Of Biotin To Streptavidin Stabilizes Intersubunit Salt Bridges Between Asp61 And His87 At Low Ph.
J. Mol. Biol. V. 274 776 1997
PubMed-ID: 9405158  |  Reference-DOI: 10.1006/JMBI.1997.1444
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STREPTAVIDIN
    Chains: B, D
    Organism Scientific: STREPTOMYCES AVIDINII
    Organism Taxid: 1895

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : BD
Biological Unit 1 (2x): BD
Biological Unit 2 (4x): BD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FMT3Ligand/IonFORMIC ACID
2GLL2Ligand/IonGLYCOLURIL
Biological Unit 1 (2, 10)
No.NameCountTypeFull Name
1FMT6Ligand/IonFORMIC ACID
2GLL4Ligand/IonGLYCOLURIL
Biological Unit 2 (2, 20)
No.NameCountTypeFull Name
1FMT12Ligand/IonFORMIC ACID
2GLL8Ligand/IonGLYCOLURIL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:23 , LEU B:25 , SER B:27 , TYR B:43 , SER B:45 , VAL B:47 , THR B:90 , TRP B:108 , LEU B:110 , ASP B:128 , FMT B:1567 , TRP D:120BINDING SITE FOR RESIDUE GLL B 300
2AC2SOFTWARETRP B:120 , ASN D:23 , LEU D:25 , SER D:27 , TYR D:43 , SER D:45 , VAL D:47 , THR D:90 , TRP D:108 , LEU D:110 , ASP D:128 , FMT D:1615BINDING SITE FOR RESIDUE GLL D 300
3AC3SOFTWARESER B:45 , VAL B:47 , TRP B:79 , LEU B:110 , GLL B:300 , FMT B:1621BINDING SITE FOR RESIDUE FMT B 1567
4AC4SOFTWAREVAL D:47 , GLY D:48 , ASN D:49 , SER D:88 , GLL D:300BINDING SITE FOR RESIDUE FMT D 1615
5AC5SOFTWAREASN B:49 , TRP B:79 , SER B:88 , LEU B:110 , FMT B:1567BINDING SITE FOR RESIDUE FMT B 1621

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.SAV_STRAV37-159
 		  2B:13-135
D:13-133
2AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 		  2B:118-132
D:118-132
Biological Unit 1 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.SAV_STRAV37-159
 		  4B:13-135
D:13-133
2AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 		  4B:118-132
D:118-132
Biological Unit 2 (2, 16)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AVIDIN_2PS51326 Avidin-like domain profile.SAV_STRAV37-159
 		  8B:13-135
D:13-133
2AVIDIN_1PS00577 Avidin-like domain signature.SAV_STRAV142-156
 		  8B:118-132
D:118-132

(-) Exons   (0, 0)

(no "Exon" information available for 2RTI)

(-) 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 B from PDB  Type:PROTEIN  Length:123
 aligned with SAV_STRAV | P22629 from UniProtKB/Swiss-Prot  Length:183

    Alignment length:123
                                    46        56        66        76        86        96       106       116       126       136       146       156   
            SAV_STRAV    37 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 159
               SCOP domains d2rtib_ B: Streptavidin                                                                                                     SCOP domains
               CATH domains 2rtiB00 B:13-135  [code=2.40.128.30, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhh.eeeee....eeeeee....eeeeeee.........eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee......hhh.eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: B:13-135 UniProt: 37-159                                                                                     PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       --- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rti B  13 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKVKP 135
                                    22        32        42        52        62        72        82        92       102       112       122       132   


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

    Alignment length:121
                                    46        56        66        76        86        96       106       116       126       136       146       156 
            SAV_STRAV    37 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 157
               SCOP domains d2rtid_ D: Streptavidin                                                                                                   SCOP domains
               CATH domains 2rtiD00 D:13-133  [code=2.40.128.30, no name defined]                                                                     CATH domains
           Pfam domains (1) --Avidin-2rtiD01 D:15-132                                                                                               - Pfam domains (1)
           Pfam domains (2) --Avidin-2rtiD02 D:15-132                                                                                               - Pfam domains (2)
         Sec.struct. author .hhhh.eeee.....eeeeee....eeeeeee.........eeeeeee..........eeeeeeee.........eeeeeeeeee.....eeeeeeeeee...hhhhhh.eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) AVIDIN_2  PDB: D:13-133 UniProt: 37-159                                                                                   PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------AVIDIN_1       - PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rti D  13 AEAGITGTWYNQLGSTFIVTAGADGALTGTYESAVGNAESRYVLTGRYDSAPATDGSGTALGWTVAWKNNYRNAHSATTWSGQYVGGAEARINTQWLLTSGTTEANAWKSTLVGHDTFTKV 133
                                    22        32        42        52        62        72        82        92       102       112       122       132
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain B,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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  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 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

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