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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STATIONARY PHASE SURVIVAL PROTEIN SURE FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH MAGNESIUM AND TUNGSTATE
 
Authors :  W. Iwasaki, K. Miki
Date :  26 Dec 06  (Deposition) - 28 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
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, Complex With Magnesium And Tungstate Ions, 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  (4, 20)

Asymmetric Unit (4, 20)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG4Ligand/IonMAGNESIUM ION
3SO410Ligand/IonSULFATE ION
4WO44Ligand/IonTUNGSTATE(VI)ION
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO410Ligand/IonSULFATE ION
4WO44Ligand/IonTUNGSTATE(VI)ION
Biological Unit 2 (3, 32)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO420Ligand/IonSULFATE ION
4WO48Ligand/IonTUNGSTATE(VI)ION
Biological Unit 3 (3, 32)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SO420Ligand/IonSULFATE ION
4WO48Ligand/IonTUNGSTATE(VI)ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:8 , ASP A:9 , ASN A:96 , WO4 A:302BINDING SITE FOR RESIDUE MG A 301
02AC2SOFTWAREASP A:8 , ASN A:96 , ASN A:100 , SER A:108 , GLY A:109 , THR A:110 , MG A:301BINDING SITE FOR RESIDUE WO4 A 302
03AC3SOFTWAREGLY A:102 , HIS A:103 , SER A:178 , VAL A:179 , ARG A:180 , TYR A:182 , ARG A:214 , HOH A:513BINDING SITE FOR RESIDUE SO4 A 401
04AC4SOFTWAREARG A:180 , ARG A:214BINDING SITE FOR RESIDUE SO4 A 402
05AC5SOFTWAREARG A:228 , LEU A:229 , ASP A:230BINDING SITE FOR RESIDUE SO4 A 403
06AC6SOFTWARETHR A:235 , ARG A:236 , PRO A:239 , THR A:240 , HOH A:510BINDING SITE FOR RESIDUE SO4 A 404
07AC7SOFTWAREASP B:8 , ASP B:9 , ASN B:96 , WO4 B:1302BINDING SITE FOR RESIDUE MG B 1301
08AC8SOFTWAREASP B:8 , ASN B:96 , ASN B:100 , SER B:108 , GLY B:109 , THR B:110 , MG B:1301 , HOH B:1427BINDING SITE FOR RESIDUE WO4 B 1302
09AC9SOFTWAREGLY B:102 , HIS B:103 , SER B:178 , ARG B:180 , TYR B:182 , ARG B:214BINDING SITE FOR RESIDUE SO4 B 1401
10BC1SOFTWAREARG B:180 , HOH B:1430BINDING SITE FOR RESIDUE SO4 B 1402
11BC2SOFTWAREILE A:45 , GLN A:116 , HIS B:103 , PRO B:202BINDING SITE FOR RESIDUE SO4 B 1403
12BC3SOFTWAREASP C:8 , ASP C:9 , ASN C:96 , WO4 C:2302BINDING SITE FOR RESIDUE MG C 2301
13BC4SOFTWAREASP C:8 , ASN C:96 , ASN C:100 , SER C:108 , GLY C:109 , THR C:110 , MG C:2301BINDING SITE FOR RESIDUE WO4 C 2302
14BC5SOFTWAREGLY C:102 , HIS C:103 , SER C:178 , ARG C:180 , TYR C:182 , ARG C:214 , HOH C:2416BINDING SITE FOR RESIDUE SO4 C 2401
15BC6SOFTWAREASP D:8 , ASP D:9 , ASN D:96 , WO4 D:3302BINDING SITE FOR RESIDUE MG D 3301
16BC7SOFTWAREASP D:8 , ASN D:96 , ASN D:100 , SER D:108 , GLY D:109 , THR D:110 , MG D:3301BINDING SITE FOR RESIDUE WO4 D 3302
17BC8SOFTWAREGLY D:102 , HIS D:103 , SER D:178 , ARG D:180 , TYR D:182 , ARG D:214BINDING SITE FOR RESIDUE SO4 D 3401
18BC9SOFTWAREARG D:180BINDING SITE FOR RESIDUE SO4 D 3402
19CC1SOFTWARESER A:24 , VAL A:29 , HIS A:64 , PRO A:66BINDING SITE FOR RESIDUE GOL A 501
20CC2SOFTWAREVAL B:29 , PRO B:55 , HIS B:64BINDING SITE FOR RESIDUE GOL B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E6B)

(-) 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 2E6B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E6B)

(-) Exons   (0, 0)

(no "Exon" information available for 2E6B)

(-) 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: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 d2e6ba_ A: automated matches                                                                                                                                                                                                                       SCOP domains
               CATH domains 2e6bA00 A:1-242  [code=3.40.1210.10,      no name defined]                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee..-----...........eee...........eeee..hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhh.eeeeee................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e6b A   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDT-----GHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTLA 242
                                    10        20        30     |   - |      50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240  
                                                              36    42                                                                                                                                                                                                        

Chain B from PDB  Type:PROTEIN  Length:233
 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 d2e6bb_ B: automated matches                                                                                                                                                                                                                      SCOP domains
               CATH domains 2e6bB00 B:1-241  [code=3.40.1210.10,       no name defined]                                                                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...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
                 2e6b B   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDT------HAITIAHPVRAYPHPSPL--PHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQPTL 241
                                    10        20        30     |   -  |     50        60  |     70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 
                                                              36     43               60 63                                                                                                                                                                                  

Chain C from PDB  Type:PROTEIN  Length:232
 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 d2e6bc_ C: automated matches                                                                                                                                                                                                                   SCOP domains
               CATH domains 2e6bC00 C:1-238  [code=3.40.1210.10,       no name defined]                                                                                                                                                                                    CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee..------..........eeee..........eeee..hhhhhhhhhhhhh....eeeeeeee...hhhhhh.hhhhhhhhhhhhh..eeeeeee...........hhhhhhhhhhhhh......eeeee.......eee.......ee..eeeee.....eeeee..ee.......hhhhhhhh..eeeee......hhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e6b C   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDT------HAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRLQ 238
                                    10        20        30     |   -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        
                                                              36     43                                                                                                                                                                                                   

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

    Alignment length:237
                                    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 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDTEQSAAGHAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRL 237
               SCOP domains d2e6bd_ D: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains 2e6bD00 D:1-237  [code=3.40.1210.10,       no name defined]                                                                                                                                                                                   CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee......hhhhhhhhhhhh...eeeeeee..------........eeeee...........eeeee.hhhhhhhhhhhhh....eeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhh......eeeee......eeee.......ee..eeeee.....eeeee..ee.......hhhhhhhhheeeeee......hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e6b D   1 MRILVTNDDGIYSPGLWALAEAASQFGEVFVAAPDT------HAITIAHPVRAYPHPSPLHAPHFPAYRVRGTPADCVALGLHLFGPVDLVLSGVNLGSNLGHEIWHSGTVAAAKQGYLFGLSAAAFSVPLNGEVPDFAGLRPWLLRTLETLLRLERPFLVNVNLPLRPKGFLWTRQSVRAYEGVVIPGEDPMGRPFYWFAPRPLKEAEEGTDRWAVAQGFVSATPLRLDLTDETRL 237
                                    10        20        30     |   -  |     50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       
                                                              36     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 2E6B)

(-) 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 | Q53W922e69 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
2e69 SURE FROM THERMUS THERMOPHILUS HB8 COMPLEXED WITH SULFATE.
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.