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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STATIONARY PHASE SURVIVAL PROTEIN SURE FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH SULFATE
 
Authors :  W. Iwasaki, K. Miki
Date :  26 Dec 06  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B,C,D  (2x)
Biol. Unit 3:  A,B,C,D  (2x)
Keywords :  Sure Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Iwasaki, K. Miki
Crystal Structure Of The Stationary Phase Survival Protein Sure With Metal Ion And Amp
J. Mol. Biol. V. 371 123 2007
PubMed-ID: 17561111  |  Reference-DOI: 10.1016/J.JMB.2007.05.007

(-) Compounds

Molecule 1 - 5'-NUCLEOTIDASE SURE
    ChainsA, B, C, D
    EC Number3.1.3.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET11A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificTHERMUS THERMOPHILUS
    Organism Taxid300852
    StrainHB8
    SynonymSTATIONARY PHASE SURVIVAL PROTEIN SURE, NUCLEOSIDE 5'- MONOPHOSPHATE PHOSPHOHYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)ABCD
Biological Unit 2 (2x)ABCD
Biological Unit 3 (2x)ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO414Ligand/IonSULFATE ION
Biological Unit 1 (2, 16)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2SO414Ligand/IonSULFATE ION
Biological Unit 2 (2, 32)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO428Ligand/IonSULFATE ION
Biological Unit 3 (2, 32)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2SO428Ligand/IonSULFATE ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:8 , ASN A:96 , ASN A:100 , SER A:108 , GLY A:109 , THR A:110 , HOH A:417BINDING SITE FOR RESIDUE SO4 A 301
02AC2SOFTWAREGLY A:102 , HIS A:103 , SER A:178 , VAL A:179 , ARG A:180 , TYR A:182 , ARG A:214 , HOH A:460BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:180 , HOH A:426BINDING SITE FOR RESIDUE SO4 A 303
04AC4SOFTWAREARG A:228 , LEU A:229 , ASP A:230 , HOH A:455 , HOH A:467 , HOH B:432BINDING SITE FOR RESIDUE SO4 A 304
05AC5SOFTWARETHR A:235 , ARG A:236 , PRO A:239 , THR A:240 , HOH A:406BINDING SITE FOR RESIDUE SO4 A 305
06AC6SOFTWAREASP B:8 , ASN B:96 , ASN B:100 , SER B:108 , GLY B:109 , THR B:110 , HOH B:426BINDING SITE FOR RESIDUE SO4 B 306
07AC7SOFTWAREGLY B:102 , HIS B:103 , SER B:178 , ARG B:180 , TYR B:182 , ARG B:214 , HOH B:430BINDING SITE FOR RESIDUE SO4 B 307
08AC8SOFTWAREARG B:180 , HOH B:434BINDING SITE FOR RESIDUE SO4 B 308
09AC9SOFTWAREILE A:45 , GLN A:116 , HIS B:103 , PRO B:202BINDING SITE FOR RESIDUE SO4 B 309
10BC1SOFTWAREASP C:8 , ASN C:96 , ASN C:100 , SER C:108 , GLY C:109 , THR C:110 , HOH C:327BINDING SITE FOR RESIDUE SO4 C 310
11BC2SOFTWAREGLY C:102 , HIS C:103 , SER C:178 , ARG C:180 , TYR C:182 , ARG C:214 , HOH C:317BINDING SITE FOR RESIDUE SO4 C 311
12BC3SOFTWAREASP D:8 , ASN D:96 , ASN D:100 , SER D:108 , GLY D:109 , THR D:110 , HOH D:323BINDING SITE FOR RESIDUE SO4 D 312
13BC4SOFTWAREGLY D:102 , HIS D:103 , SER D:178 , VAL D:179 , ARG D:180 , TYR D:182 , ARG D:214 , HOH D:355BINDING SITE FOR RESIDUE SO4 D 313
14BC5SOFTWAREARG D:180 , HOH D:334BINDING SITE FOR RESIDUE SO4 D 314
15BC6SOFTWARESER A:24 , GLY A:27 , GLU A:28 , VAL A:29 , PRO A:66BINDING SITE FOR RESIDUE GOL A 401
16BC7SOFTWAREGLU B:28 , VAL B:29 , PRO B:55 , HIS B:64 , HOH B:424BINDING SITE FOR RESIDUE GOL B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E69)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric Unit
No.Residues
1Gly A:86 -Pro A:87
2Gly A:94 -Val A:95
3Arg A:157 -Pro A:158
4Gly B:86 -Pro B:87
5Gly B:94 -Val B:95
6Arg B:157 -Pro B:158
7Gly C:86 -Pro C:87
8Gly C:94 -Val C:95
9Arg C:157 -Pro C:158
10Gly D:86 -Pro D:87
11Gly D:94 -Val D:95
12Arg D:157 -Pro D:158

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E69)

(-) Exons   (0, 0)

(no "Exon" information available for 2E69)

(-) 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:237
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:243
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAH 243
               SCOP domains d2e69a_ A: automated matches                                                                                                                                                                                                                        SCOP domains
               CATH domains 2e69A00 A:1-243  [code=3.40.1210.10      , no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh..eeeeeee.------..........eeee...........eeeee.hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhh....eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e69 A   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPD------GHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLAH 243
                                    10        20        30    |    - |      50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240   
                                                             35     42                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:232
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:242
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLA 242
               SCOP domains d2e69b_ B: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2e69B00 B:1-242  [code=3.40.1210.10       , no name defined   ]                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhhh..eeeeeee.-------..........eee....---....eeee..hhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee......hhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e69 B   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPD-------HAITIAHPVRAYPHPSP---PHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLA 242
                                    10        20        30    |    -  |     50        |-  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
                                                             35      43              59  63                                                                                                                                                                                   

Chain C from PDB  Type:PROTEIN  Length:231
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:238
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQ 238
               SCOP domains d2e69c_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2e69C00 C:1-238  [code=3.40.1210.10       , no name defined]                                                                                                                                                                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee.-------.........eeee...........eeeee.hhhhhhhhhhhhhh...eeeeeeee...hhhhhh.hhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee.......eee.......ee..eeeee.....eeeee..ee.......hhhhhhhh..eeeee......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e69 C   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPD-------HAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQ 238
                                    10        20        30    |    -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
                                                             35      43                                                                                                                                                                                                   

Chain D from PDB  Type:PROTEIN  Length:234
 aligned with SURE_THET8 | Q53W92 from UniProtKB/Swiss-Prot  Length:244

    Alignment length:241
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
           SURE_THET8     1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTL 241
               SCOP domains d2e69d_ D: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 2e69D00 D:1-241  [code=3.40.1210.10       , no name defined]                                                                                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee.-------........eeeee...........eeee..hhhhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee......hhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e69 D   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPD-------HAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTL 241
                                    10        20        30    |    -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
                                                             35      43                                                                                                                                                                                                      

   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 Unit

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E69)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (SURE_THET8 | Q53W92)
molecular function
    GO:0008253    5'-nucleotidase activity    Catalysis of the reaction: a 5'-ribonucleotide + H2O = a ribonucleoside + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008252    nucleotidase activity    Catalysis of the reaction: a nucleotide + H2O = a nucleoside + phosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SURE_THET8 | Q53W922e6b 2e6c 2e6e 2e6g 2e6h

(-) Related Entries Specified in the PDB File

1ilv SURE FROM THERMATOGA MARITIMA
1j9j SURE FROM THERMATOGA MARITIMA
1j9k SURE FROM THERMATOGA MARITIMA COMPLEXED WITH CALCIUM AND TUNGSTATE.
1j9l SURE FROM THERMATOGA MARITIMA COMPLEXED WITH CALCIUM AND VANADATE.
1l5x SURE HOMOLOG FROM PYROBACULUM AEROPHILUM
2e6b SURE FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH MAGNESIUM AND TUNGSTATE.
2e6c SURE FROM THERMUS THERMOPHILUS HB8 COCRYSTALLIZED WITH MANGANESE AND AMP.
2e6e SURE FROM THERMUS THERMOPHILUS HB8.
2e6g SURE FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH PHOSPHATE.
2e6h E37A MUTANT OF SURE FROM THERMUS THERMOPHILUS HB8 COCRYSTALLIZED WITH MANGANESE AND AMP.