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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ALDEHYDE DEHYDROGENASE (A.K.A. AOR OR MOP) OF DESULFOVIBRIO GIGAS COVALENTLY BOUND TO [ASO3]-
 
Authors :  D. R. Boer, M. J. Romao
Date :  21 Dec 09  (Deposition) - 16 Feb 10  (Release) - 16 Feb 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Molybdenum-Containing Enzymes, Aldehyde Oxidoreductase, Xanthine Oxidase Family, Reduced Form, Arsenite Inhibition, 2Fe-2S, Fad, Flavoprotein, Iron, Iron-Sulfur, Metal- Binding, Molybdenum, Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Thapper, D. R. Boer, C. D. Brondino, J. J. Moura, M. J. Romao
Correlating Epr And X-Ray Structural Analysis Of Arsenite-Inhibited Forms Of Aldehyde Oxidoreductase.
J. Biol. Inorg. Chem. V. 12 353 2007
PubMed-ID: 17139522  |  Reference-DOI: 10.1007/S00775-006-0191-9

(-) Compounds

Molecule 1 - ALDEHYDE OXIDOREDUCTASE
    ChainsA
    EC Number1.2.99.7
    Organism ScientificDESULFOVIBRIO GIGAS
    Organism Taxid879
    SynonymMOLYBDENUM IRON SULFUR PROTEIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 24)

Asymmetric Unit (9, 24)
No.NameCountTypeFull Name
1AST1Ligand/IonARSENITE
2CA1Ligand/IonCALCIUM ION
3CL9Ligand/IonCHLORIDE ION
4FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5IPA3Ligand/IonISOPROPYL ALCOHOL
6LI1Ligand/IonLITHIUM ION
7MG5Ligand/IonMAGNESIUM ION
8PCD1Ligand/Ion(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
9URE1Ligand/IonUREA
Biological Unit 1 (5, 8)
No.NameCountTypeFull Name
1AST1Ligand/IonARSENITE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4FES2Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5IPA3Ligand/IonISOPROPYL ALCOHOL
6LI-1Ligand/IonLITHIUM ION
7MG-1Ligand/IonMAGNESIUM ION
8PCD1Ligand/Ion(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
9URE1Ligand/IonUREA
Biological Unit 2 (5, 16)
No.NameCountTypeFull Name
1AST2Ligand/IonARSENITE
2CA-1Ligand/IonCALCIUM ION
3CL-1Ligand/IonCHLORIDE ION
4FES4Ligand/IonFE2/S2 (INORGANIC) CLUSTER
5IPA6Ligand/IonISOPROPYL ALCOHOL
6LI-1Ligand/IonLITHIUM ION
7MG-1Ligand/IonMAGNESIUM ION
8PCD2Ligand/Ion(MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V)
9URE2Ligand/IonUREA

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:99 , CYS A:100 , GLY A:101 , CYS A:103 , CYS A:137 , ARG A:138 , CYS A:139 , ILE A:368BINDING SITE FOR RESIDUE FES A 908
02AC2SOFTWAREGLY A:39 , CYS A:40 , GLU A:41 , GLY A:43 , GLN A:44 , CYS A:45 , GLY A:46 , CYS A:48 , ARG A:58 , CYS A:60BINDING SITE FOR RESIDUE FES A 909
03AC3SOFTWAREHOH A:1391 , HOH A:1568 , HOH A:1760 , HOH A:1937 , HOH A:1938 , HOH A:2272BINDING SITE FOR RESIDUE MG A 910
04AC4SOFTWAREHOH A:1260 , HOH A:1750 , HOH A:1831 , HOH A:1843 , HOH A:1983 , HOH A:1984BINDING SITE FOR RESIDUE MG A 911
05AC5SOFTWAREHOH A:1395 , HOH A:1677 , HOH A:1708 , HOH A:1710 , HOH A:1828 , HOH A:1900BINDING SITE FOR RESIDUE MG A 912
06AC6SOFTWAREASP A:263 , GLU A:899 , GLU A:903 , HOH A:1723 , HOH A:1727 , HOH A:2813BINDING SITE FOR RESIDUE MG A 913
07AC7SOFTWAREHOH A:1337 , HOH A:1467 , HOH A:1647 , HOH A:1721 , HOH A:2611 , HOH A:2612BINDING SITE FOR RESIDUE MG A 914
08AC8SOFTWAREALA A:649 , GLU A:651 , GLY A:693 , HOH A:1243BINDING SITE FOR RESIDUE LI A 915
09AC9SOFTWAREPRO A:258 , THR A:259 , ALA A:755 , HOH A:1438 , HOH A:2296BINDING SITE FOR RESIDUE CL A 916
10BC1SOFTWAREPHE A:167 , SER A:178 , LYS A:179 , HOH A:1331 , HOH A:1765BINDING SITE FOR RESIDUE CL A 917
11BC2SOFTWAREARG A:123 , LYS A:605BINDING SITE FOR RESIDUE CL A 918
12BC3SOFTWARETYR A:892 , ARG A:893 , HOH A:1664BINDING SITE FOR RESIDUE CL A 919
13BC4SOFTWARELYS A:248 , PRO A:898 , GLU A:899BINDING SITE FOR RESIDUE CL A 920
14BC5SOFTWARELYS A:473 , ASP A:474BINDING SITE FOR RESIDUE CL A 921
15BC6SOFTWAREMET A:1 , ALA A:19BINDING SITE FOR RESIDUE CL A 923
16BC7SOFTWAREASP A:342 , THR A:343 , GLY A:344BINDING SITE FOR RESIDUE CL A 925
17BC8SOFTWAREARG A:460 , SER A:461 , LEU A:498 , ALA A:531 , PHE A:532 , TYR A:535 , GLY A:536 , GLN A:539 , HOH A:957BINDING SITE FOR RESIDUE URE A 926
18BC9SOFTWAREASP A:826 , ILE A:827 , LYS A:828 , LYS A:829 , HOH A:2595 , HOH A:2596BINDING SITE FOR RESIDUE CL A 930
19CC1SOFTWAREGLN A:99 , CYS A:139 , GLY A:419 , THR A:420 , PHE A:421 , GLY A:422 , ALA A:531 , PHE A:532 , ARG A:533 , TRP A:650 , HIS A:653 , GLY A:654 , GLN A:655 , GLY A:656 , GLY A:660 , SER A:695 , GLY A:696 , GLY A:697 , ARG A:699 , GLN A:700 , GLN A:701 , LEU A:795 , SER A:797 , CYS A:799 , ASN A:800 , THR A:804 , GLN A:807 , ALA A:864 , SER A:865 , GLY A:866 , VAL A:867 , GLY A:868 , GLU A:869 , AST A:932 , IPA A:933 , HOH A:1409 , HOH A:2814BINDING SITE FOR RESIDUE PCD A 931
20CC2SOFTWARETYR A:535 , TYR A:622 , GLY A:696 , GLY A:697 , GLU A:869 , PCD A:931 , HOH A:1236BINDING SITE FOR RESIDUE AST A 932
21CC3SOFTWARETYR A:535 , LEU A:626 , GLY A:697 , PCD A:931 , HOH A:1236BINDING SITE FOR RESIDUE IPA A 933
22CC4SOFTWAREASN A:691 , HOH A:1012BINDING SITE FOR RESIDUE IPA A 934
23CC5SOFTWARELEU A:626BINDING SITE FOR RESIDUE IPA A 935
24CC6SOFTWAREASP A:288 , HOH A:1935BINDING SITE FOR RESIDUE CA A 1457

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L4P)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu A:894 -Pro A:895

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L4P)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.MOP_DESGI2-79  1A:2-79
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.MOP_DESGI40-48  1A:40-48
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.MOP_DESGI2-79  1A:2-79
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.MOP_DESGI40-48  1A:40-48
Biological Unit 2 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
12FE2S_FER_2PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.MOP_DESGI2-79  2A:2-79
22FE2S_FER_1PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.MOP_DESGI40-48  2A:40-48

(-) Exons   (0, 0)

(no "Exon" information available for 3L4P)

(-) 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:907
 aligned with MOP_DESGI | Q46509 from UniProtKB/Swiss-Prot  Length:907

    Alignment length:907
                                    10        20        30        40        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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       
            MOP_DESGI     1 MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSVILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQCGFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLGLKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNRITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKVKVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASADVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIAPGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNYQQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTLRGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDMLAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAWEDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGATHCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCNQLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDIVYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEKVLEALKA 907
               SCOP domains d3l4pa2 A:1-80 Aldehyde oxidoreductase, N-terminal domain                       d3l4pa1 A:81-193 Aldehyde oxidoreductase, domain 2                                                               d3l4pa3 A:194-310 Aldehyde oxidoreductase, domain 3                                                                  d3l4pa4 A:311-907 Aldehyde oxidoreductase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3l4pA01 A:1-74  [code=3.10.20.30, no name defined]                        3l4pA02 A:75-193  [code=1.10.150.120, no name defined]                                                                 --------------3l4pA03 A:208-308  [code=3.90.1170.50, no name defined]                                              ----------------------3l4pA04 A:331-364,A:458-580       3l4pA05 A:365-457 Aldehyde Oxidoreductase; domain 4                                          3l4pA04 A:331-364,A:458-580 Aldehyde Oxidoreductase; domain 4                                                              3l4pA06 A:581-624,A:751-907                 3l4pA07 A:625-750 Aldehyde Oxidoreductase; domain 4                                                                           3l4pA06 A:581-624,A:751-907 Aldehyde Oxidoreductase; domain 4                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..eeeeeee....hhhhhhhhh..................eeee..eeee.hhhhhhhh....eeehhhhhh.....hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhhhhhh...hhhhhh.................hhhhhhh....hhhhhhhh.....eeeeeee.....eeeeeeehhhhhh...eeeeehhhhh....ee...............ee.....ee.....eeeeeee.hhhhhhhhhh..eeeeee.....hhhhhhh............eeeeeeeee..hhhhhhhhh.eeeeeeeee...........eeeeee.....eeeee...hhhhhhhhhhhhhh.hhh.eeeee.......hhhhh..hhhhhhhhhhhhh..eeee.hhhhhhhh......eeeeeeeee.....eeeeeeeeeee......hhhhhhhhhhhhh.......eeeeeeeee.............hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeee.......eeeeeeee.....eeee........hhhhhhhhhhhhhhhhhh.hhh.eee.................hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhh....eeeeeee...................eeeeeeeeeeeee.....eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhh..................hhhhh...eeeee.......hhhhh....hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -2FE2S_FER_2  PDB: A:2-79 UniProt: 2-79                                        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------2FE2S_FER------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3l4p A   1 MIQKVITVNGIEQNLFVDAEALLSDVLRQQLGLTGVKVGCEQGQCGACSVILDGKVVRACVTKMKRVADGAQITTIEGVGQPENLHPLQKAWVLHGGAQCGFCSPGFIVSAKGLLDTNADPSREDVRDWFQKHRNACRCTGYKPLVDAVMDAAAVINGKKPETDLEFKMPADGRIWGSKYPRPTAVAKVTGTLDYGADLGLKMPAGTLHLAMVQAKVSHANIKGIDTSEALTMPGVHSVITHKDVKGKNRITGLITFPTNKGDGWDRPILCDEKVFQYGDCIALVCADSEANARAAAEKVKVDLEELPAYMSGPAAAAEDAIEIHPGTPNVYFEQPIVKGEDTGPIFASADVTVEGDFYVGRQPHMPIEPDVAFAYMGDDGKCYIHSKSIGVHLHLYMIAPGVGLEPDQLVLVANPMGGTFGYKFSPTSEALVAVAAMATGRPVHLRYNYQQQQQYTGKRSPWEMNVKFAAKKDGTLLAMESDWLVDHGPYSEFGDLLTLRGAQFIGAGYNIPNIRGLGRTVATNHVWGSAFRGYGAPQSMFASECLMDMLAEKLGMDPLELRYKNAYRPGDTNPTGQEPEVFSLPDMIDQLRPKYQAALEKAQKESTATHKKGVGISIGVYGSGLDGPDASEAWAELNADGTITVHTAWEDHGQGADIGCVGTAHEALRPMGVAPEKIKFTWPNTATTPNSGPSGGSRQQVMTGNAIRVACENLLKACEKPGGGYYTYDELKAADKPTKITGNWTASGATHCDAVTGLGKPFVVYMYGVFMAEVTVDVATGQTTVDGMTLMADLGSLCNQLATDGQIYGGLAQGIGLALSEDFEDIKKHATLVGAGFPFIKQIPDKLDIVYVNHPRPDGPFGASGVGELPLTSPHAAIINAIKSATGVRIYRLPAYPEKVLEALKA 907
                                    10        20        30        40        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       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880       890       900       

   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  (4, 4)

Asymmetric Unit

(-) CATH Domains  (4, 7)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3L4P)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A   (MOP_DESGI | Q46509)
molecular function
    GO:0051537    2 iron, 2 sulfur cluster binding    Interacting selectively and non-covalently with a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
    GO:0033727    aldehyde dehydrogenase (FAD-independent) activity    Catalysis of the reaction: an aldehyde + H2O + acceptor = a carboxylate + reduced acceptor.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0051536    iron-sulfur cluster binding    Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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  MOP_DESGI | Q46509
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 Related Entries

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

UniProtKB/Swiss-Prot
        MOP_DESGI | Q465091sij 1vlb 3fah 3fc4 4c7y 4c7z 4c80 4us8 4us9 4usa

(-) Related Entries Specified in the PDB File

1dgj A CLOSELY RELATED PROTEIN FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 (UNINHIBITED FORM)
1sij ARSENITE INHIBITED, NON-REDUCED FORM OF D. GIGAS ADH
1vlb THE SAME PROTEIN (AHD FROM DESULFOVIBRIO GIGAS) IN ITS UNINHIBITED FORM (NO ARSENITE BOUND) REFINED AT HIGH RESOLUTION
3fah GLYCEROL INHIBITED FORM OF THE D. GIGAS ADH
3fc4 ETHYLENE GLYCOL INHIBITED FORM OF THE D. GIGAS ADH