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(-) Description

Title :  THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE
 
Authors :  M. E. M. Noble, A. Cleasby, L. N. Johnson, M. Egmond, L. G. J. Frenken
Date :  21 Dec 93  (Deposition) - 31 May 94  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  D  (1x)
Biol. Unit 3:  A  (1x)
Biol. Unit 4:  C  (1x)
Keywords :  Hydrolase(Carboxylic Esterase) (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. E. Noble, A. Cleasby, L. N. Johnson, M. R. Egmond, L. G. Frenken
The Crystal Structure Of Triacylglycerol Lipase From Pseudomonas Glumae Reveals A Partially Redundant Catalytic Aspartate.
Febs Lett. V. 331 123 1993
PubMed-ID: 8405390  |  Reference-DOI: 10.1016/0014-5793(93)80310-Q
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - LIPASE
    ChainsB, A, C, D
    EC Number3.1.1.3
    EngineeredYES
    Organism ScientificBURKHOLDERIA GLUMAE
    Organism Taxid337

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x) B  
Biological Unit 2 (1x)   D
Biological Unit 3 (1x)A   
Biological Unit 4 (1x)  C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP B:241 , ASP B:287 , GLN B:291 , VAL B:295BINDING SITE FOR RESIDUE CA B 320
02AC2SOFTWAREASP A:241 , ASP A:287 , GLN A:291 , VAL A:295BINDING SITE FOR RESIDUE CA A 320
03AC3SOFTWAREASP C:241 , ASP C:287 , GLN C:291 , VAL C:295BINDING SITE FOR RESIDUE CA C 320
04AC4SOFTWAREASP D:241 , ASP D:287 , GLN D:291 , VAL D:295BINDING SITE FOR RESIDUE CA D 320
05ACAAUTHORSER A:87 , HIS A:285 , ASP A:263 , GLU A:288ACTIVE SITE
06ACBAUTHORSER B:87 , HIS B:285 , ASP B:263 , GLU B:288ACTIVE SITE
07ACCAUTHORSER C:87 , HIS C:285 , ASP C:263 , GLU C:288ACTIVE SITE
08ACDAUTHORSER D:87 , HIS D:285 , ASP D:263 , GLU D:288ACTIVE SITE
09CAAAUTHORASP A:287 , GLN A:291 , ASP A:241 , VAL A:295CALCIUM SITE NEAR TO THE ACTIVE SITE
10CABAUTHORASP B:287 , GLN B:291 , ASP B:241 , VAL B:295CALCIUM SITE NEAR TO THE ACTIVE SITE
11CACAUTHORASP C:287 , GLN C:291 , ASP C:241 , VAL C:295CALCIUM SITE NEAR TO THE ACTIVE SITE
12CADAUTHORASP D:287 , GLN D:291 , ASP D:241 , VAL D:295CALCIUM SITE NEAR TO THE ACTIVE SITE

(-) SS Bonds  (4, 4)

Asymmetric Unit
No.Residues
1A:190 -A:269
2B:190 -B:269
3C:190 -C:269
4D:190 -D:269

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_BURGL120-129
 
 
 
  4A:81-90
B:81-90
C:81-90
D:81-90
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_BURGL120-129
 
 
 
  1-
B:81-90
-
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_BURGL120-129
 
 
 
  1-
-
-
D:81-90
Biological Unit 3 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_BURGL120-129
 
 
 
  1A:81-90
-
-
-
Biological Unit 4 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPASE_SERPS00120 Lipases, serine active site.LIP_BURGL120-129
 
 
 
  1-
-
C:81-90
-

(-) Exons   (0, 0)

(no "Exon" information available for 1TAH)

(-) 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:318
 aligned with LIP_BURGL | Q05489 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
            LIP_BURGL    41 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 358
               SCOP domains d1taha_ A: Lipase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1tahA00 A:2-319  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee..................hhhhhhh....eeee.............hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.hhheeeeeee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhh...hhhhhhhhhh.................eeee..eeeeeeee....eeeeeee..eeeeee........hhhh..hhhhhhhhhhhhh............hhhh...ee..........hhh.............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tah A   2 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        

Chain B from PDB  Type:PROTEIN  Length:318
 aligned with LIP_BURGL | Q05489 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
            LIP_BURGL    41 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 358
               SCOP domains d1tahb_ B: Lipase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1tahB00 B:2-319  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee..................hhhhhhh....eeee.............hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.hhheeeeeee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhh...hhhhhhhhhh.................eeee..eeeeeeee....eeeeeee..eeeeee........hhhh..hhhhhhhhhhhhh............hhhh...ee..........hhh.............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tah B   2 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        

Chain C from PDB  Type:PROTEIN  Length:318
 aligned with LIP_BURGL | Q05489 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
            LIP_BURGL    41 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 358
               SCOP domains d1tahc_ C: Lipase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1tahC00 C:2-319  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeee..................hhhhhhh....eeee.............hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.hhheeeeeee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhh...hhhhhhhhhh.................eeee..eeeeeeee....eeeeeee..eeeeee........hhhh..hhhhhhhhhhhhh............hhhh...ee..........hhh.............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tah C   2 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        

Chain D from PDB  Type:PROTEIN  Length:318
 aligned with LIP_BURGL | Q05489 from UniProtKB/Swiss-Prot  Length:358

    Alignment length:318
                                    50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350        
            LIP_BURGL    41 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 358
               SCOP domains d1tahd_ D: Lipase                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1tahD00 D:2-319  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                          CATH domains
           Pfam domains (1) ----------------------------------------Abhydrolase_1-1tahD01 D:42-295                                                                                                                                                                                                                                ------------------------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------Abhydrolase_1-1tahD02 D:42-295                                                                                                                                                                                                                                ------------------------ Pfam domains (2)
           Pfam domains (3) ----------------------------------------Abhydrolase_1-1tahD03 D:42-295                                                                                                                                                                                                                                ------------------------ Pfam domains (3)
           Pfam domains (4) ----------------------------------------Abhydrolase_1-1tahD04 D:42-295                                                                                                                                                                                                                                ------------------------ Pfam domains (4)
         Sec.struct. author .........eeee..................hhhhhhh....eeee.............hhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh.hhheeeeeee.......hhhhhhhhhhhh.......hhhhhhhhhhhhh.......hhhhhhhhh...hhhhhhhhhh.................eeee..eeeeeeee....eeeeeee..eeeeee........hhhh..hhhhhhhhhhhhh............hhhh...ee..........hhh.............................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------LIPASE_SER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tah D   2 DTYAATRYPVILVHGLAGTDKFANVVDYWYGIQSDLQSHGAKVYVANLSGFQSDDGPNGRGEQLLAYVKQVLAATGATKVNLIGHSQGGLTSRYVAAVAPQLVASVTTIGTPHRGSEFADFVQDVLKTDPTGLSSTVIAAFVNVFGTLVSSSHNTDQDALAALRTLTTAQTATYNRNFPSAGLGAPGSCQTGAATETVGGSQHLLYSWGGTAIQPTSTVLGVTGATDTSTGTLDVANVTDPSTLALLATGAVMINRASGQNDGLVSRCSSLFGQVISTSYHWNHLDEINQLLGVRGANAEDPVAVIRTHVNRLKLQGV 319
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311        

   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  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (LIP_BURGL | Q05489)
molecular function
    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:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004806    triglyceride lipase activity    Catalysis of the reaction: triacylglycerol + H2O = diacylglycerol + a carboxylate.
biological process
    GO:0016042    lipid catabolic process    The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
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
        LIP_BURGL | Q054891cvl 1qge 2es4

(-) Related Entries Specified in the PDB File

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