Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  METHANOL DEHYDROGENASE FROM METHYLACIDIPHILUM FUMARIOLICUM SOLV
 
Authors :  A. J. Pol, T. R. M. Barends, A. Dietl, A. F. Khadem, J. Eygenstein, M. S. M. H. J. M. Op Den Camp
Date :  16 Aug 13  (Deposition) - 18 Sep 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dehydrogenase, Pqq, Lanthanide Ion, Cerium Ion, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Pol, T. R. Barends, A. Dietl, A. F. Khadem, J. Eygensteyn, M. S. Jetten, H. J. Op Den Camp
Rare Earth Metals Are Essential For Methanotrophic Life In Volcanic Mudpots.
Environ. Microbiol. V. 16 255 2014
PubMed-ID: 24034209  |  Reference-DOI: 10.1111/1462-2920.12249

(-) Compounds

Molecule 1 - METHANOL DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.2.7, 1.1.2.8
    Fragment: UNP RESIDUES 35-611
    Organism Scientific: METHYLACIDIPHILUM FUMARIOLICUM SOLV
    Organism Taxid: 1156937

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
115P2Ligand/IonPOLYETHYLENE GLYCOL (N=34)
2CE2Ligand/IonCERIUM (III) ION
3PQQ2Ligand/IonPYRROLOQUINOLINE QUINONE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:172 , ASN A:256 , ASP A:299 , ASP A:301 , PQQ A:602 , 15P A:603BINDING SITE FOR RESIDUE CE A 601
2AC2SOFTWAREGLU A:55 , CYS A:104 , CYS A:105 , VAL A:108 , ARG A:110 , THR A:154 , SER A:169 , GLY A:170 , GLY A:171 , GLU A:172 , THR A:236 , TRP A:238 , SER A:255 , ASN A:256 , ASP A:299 , ASP A:301 , ARG A:326 , ASP A:388 , TRP A:467 , GLY A:531 , TRP A:532 , CE A:601 , 15P A:603BINDING SITE FOR RESIDUE PQQ A 602
3AC3SOFTWARECYS A:104 , CYS A:105 , GLU A:172 , TRP A:260 , ASP A:299 , TRP A:532 , CE A:601 , PQQ A:602BINDING SITE FOR RESIDUE 15P A 603
4AC4SOFTWAREGLU B:172 , ASN B:256 , ASP B:299 , ASP B:301 , PQQ B:602 , 15P B:603BINDING SITE FOR RESIDUE CE B 601
5AC5SOFTWAREGLU B:55 , CYS B:104 , CYS B:105 , VAL B:108 , ARG B:110 , THR B:154 , SER B:169 , GLY B:170 , GLY B:171 , GLU B:172 , THR B:236 , TRP B:238 , SER B:255 , ASN B:256 , ASP B:299 , ASP B:301 , ARG B:326 , ASP B:388 , TRP B:467 , GLY B:531 , TRP B:532 , CE B:601 , 15P B:603BINDING SITE FOR RESIDUE PQQ B 602
6AC6SOFTWARECYS B:104 , CYS B:105 , GLU B:172 , TRP B:260 , ASP B:299 , TRP B:532 , CE B:601 , PQQ B:602BINDING SITE FOR RESIDUE 15P B 603

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:104 -A:105
2A:380 -A:409
3B:104 -B:105
4B:380 -B:409

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Tyr A:71 -Pro A:72
2Lys A:83 -Pro A:84
3Lys A:271 -Trp A:272
4Cys A:380 -Pro A:381
5Tyr B:71 -Pro B:72
6Lys B:83 -Pro B:84
7Lys B:271 -Trp B:272
8Cys B:380 -Pro B:381

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MAE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MAE)

(-) Exons   (0, 0)

(no "Exon" information available for 4MAE)

(-) Sequences/Alignments

Asymmetric/Biological 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:577
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4maea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.................ee........hhhhheeeeeee...........eee..eeeee......eeeee......eeeeee....hhhhhhhh.........eee..eeeee....eeeeee.....eeeeee..hhhhh.......eee..eeee...........eeeeee.....eeeeee...hhhhhh........hhhhh..hhhhhh...hhhhhh........eee....eeeee.......hhhhhh........eeeee......eeeeee..................eeee..eeeeeeeee....eeeeee.....eeeeee......eeee......eee.hhhh.....eeeee.............eee....eeeeeee.eeeeeee.............eeeeeeehhhhh....eeeeeee....eeeeeeee........eee...eeeee....eeeeee.....eeeeee.........eeee.....eeeeeee......hhhhhh.......hhhhhhhhhhhhhhhhhhh....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mae A   1 NDELIKLEKEPGQWVMQNKNYANTRYSELNQINTKNVSRLRLAWSFSTGALRGHEGGPLVVGTTMYVHSAYPNHVYALDLTQKPYAIKWQYTPVQNSQAVAVACCDVVNRGLAYANGKIFMTTLDGQIIALDANTGKELWKMKHADVTKGETITGAPLVVKDKVLVGVSGGEFGVRGRVGAYDINTGNRVWLAYSQGPDEEVLLDSDFNKEFPQHGGPGDGTKTWPGEQWKLGGGTTWGWYSYDPALDLFYYGTSNPGTWNAEQRKGGDNKWSCTIFARRPDTGKARWAYQMTPWDSWDYDGVNEMILPDLTVKGKKTPCLVHFDRNGFGYVLDRRTGQLIEAQPFVYVNWAKEISKENDRPVEIPEKRTKQGVDTKGICPNSMGGKDQQPAAFSPQTGLFYVPTNNMCMNYEGVEATYTAGAPYVGANVLMYSGHEGKDDYYGAFICYDALKGKRVWEIHEHFPVWSGPVVTAGGLAFYGTMDGWFKAVDIKTGKVLWQQKLGSGIIGNPITFLGPDKKQYVAVYSGVGGWFGIAVAQNLPPDDPYAGLGAVGVAYQAGLPKATTVGGELYVFALE 577
                                    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       


Chain B from PDB  Type:PROTEIN  Length:577
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4maeb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh.................ee........hhhhheeeeeee...........eee..eeeee......eeeee......eeeeee.....hhhhhh..........eee..eeeee....eeeeee.....eeeeee..hhhhh.......eee..eeee...........eeeeee.....eeeeee...hhhhhh........hhhhh..hhhhhh...hhhhhh........eee....eeeee.......hhhhhh........eeeee......eeeeee..................eeee..eeeeeeeee....eeeeee.....eeeeee......eeee......eee.hhhh.....eeeee.............ee......eeeeee.eeeeeee.............eeeeeeehhhhh....eeeeeee....eeeeeeee........eee...eeeee....eeeeee.....eeeeee.........eeee.....eeeeeee......hhhhhh...........hhhhhhhhhhhhhh.....eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mae B   1 NDELIKLEKEPGQWVMQNKNYANTRYSELNQINTKNVSRLRLAWSFSTGALRGHEGGPLVVGTTMYVHSAYPNHVYALDLTQKPYAIKWQYTPVQNSQAVAVACCDVVNRGLAYANGKIFMTTLDGQIIALDANTGKELWKMKHADVTKGETITGAPLVVKDKVLVGVSGGEFGVRGRVGAYDINTGNRVWLAYSQGPDEEVLLDSDFNKEFPQHGGPGDGTKTWPGEQWKLGGGTTWGWYSYDPALDLFYYGTSNPGTWNAEQRKGGDNKWSCTIFARRPDTGKARWAYQMTPWDSWDYDGVNEMILPDLTVKGKKTPCLVHFDRNGFGYVLDRRTGQLIEAQPFVYVNWAKEISKENDRPVEIPEKRTKQGVDTKGICPNSMGGKDQQPAAFSPQTGLFYVPTNNMCMNYEGVEATYTAGAPYVGANVLMYSGHEGKDDYYGAFICYDALKGKRVWEIHEHFPVWSGPVVTAGGLAFYGTMDGWFKAVDIKTGKVLWQQKLGSGIIGNPITFLGPDKKQYVAVYSGVGGWFGIAVAQNLPPDDPYAGLGAVGVAYQAGLPKATTVGGELYVFALE 577
                                    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
   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, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MAE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MAE)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    15P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PQQ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Cys A:380 - Pro A:381   [ RasMol ]  
    Cys B:380 - Pro B:381   [ RasMol ]  
    Lys A:271 - Trp A:272   [ RasMol ]  
    Lys A:83 - Pro A:84   [ RasMol ]  
    Lys B:271 - Trp B:272   [ RasMol ]  
    Lys B:83 - Pro B:84   [ RasMol ]  
    Tyr A:71 - Pro A:72   [ RasMol ]  
    Tyr B:71 - Pro B:72   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4mae
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  I0JWN7_9BACT | I0JWN7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  1.1.2.7
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  1.1.2.8
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  I0JWN7_9BACT | I0JWN7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4MAE)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MAE)