Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  UPF1-RNA COMPLEX
 
Authors :  S. Chakrabarti, U. Jayachandran, F. Bonneau, F. Fiorini, C. Basquin, S H. Le Hir, E. Conti
Date :  26 Nov 10  (Deposition) - 30 Mar 11  (Release) - 30 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Keywords :  Hydrolase-Rna Complex, Nmd, Rna Degradation, Allosteric Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Chakrabarti, U. Jayachandran, F. Bonneau, F. Fiorini, C. Basquin, S. Domcke, H. Le Hir, E. Conti
Molecular Mechanisms For The Rna-Dependent Atpase Activity Of Upf1 And Its Regulation By Upf2.
Mol. Cell V. 41 693 2011
PubMed-ID: 21419344  |  Reference-DOI: 10.1016/J.MOLCEL.2011.02.010

(-) Compounds

Molecule 1 - ATP-DEPENDENT HELICASE NAM7
    Chains: A
    EC Number: 3.6.4.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3) GOLD PLYSS
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CH DOMAIN AND HELICASE DOMAIN, RESIDUES 54-850
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: UP FRAMESHIFT FACTOR 1, NONSENSE-MEDIATED MRNA DECAY PROTEIN 1, NUCLEAR ACCOMODATION OF MITOCHONDRIA 7 PROTEIN, UP-FRAMESHIFT SUPPRESSOR 1
 
Molecule 2 - 5- R(*UP*UP*UP*UP*UP*UP*UP*UP*U) -3
    Chains: B
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
11PE12Ligand/IonPENTAETHYLENE GLYCOL
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3ALF1Ligand/IonTETRAFLUOROALUMINATE ION
4MG1Ligand/IonMAGNESIUM ION
5ZN3Ligand/IonZINC ION
Biological Unit 1 (3, 14)
No.NameCountTypeFull Name
11PE12Ligand/IonPENTAETHYLENE GLYCOL
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3ALF1Ligand/IonTETRAFLUOROALUMINATE ION
4MG-1Ligand/IonMAGNESIUM ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:62 , CYS A:65 , CYS A:84 , HIS A:94BINDING SITE FOR RESIDUE ZN A1851
02AC2SOFTWARECYS A:76 , CYS A:79 , HIS A:98 , HIS A:104BINDING SITE FOR RESIDUE ZN A1852
03AC3SOFTWARECYS A:122 , CYS A:125 , CYS A:148 , CYS A:152BINDING SITE FOR RESIDUE ZN A1853
04AC4SOFTWAREGLN A:408 , GLN A:413 , GLY A:433 , THR A:434 , GLY A:435 , LYS A:436 , THR A:437 , VAL A:438 , TYR A:638 , ARG A:639 , GLU A:769 , ALF A:1855 , MG A:1856 , HOH A:2090 , HOH A:2091BINDING SITE FOR RESIDUE ADP A1854
05AC5SOFTWAREPRO A:432 , GLY A:433 , LYS A:436 , GLN A:601 , ARG A:639 , GLY A:767 , ARG A:801 , ADP A:1854 , MG A:1856 , HOH A:2047 , HOH A:2051BINDING SITE FOR RESIDUE ALF A1855
06AC6SOFTWARETHR A:437 , ADP A:1854 , ALF A:1855 , HOH A:2038 , HOH A:2047 , HOH A:2090BINDING SITE FOR RESIDUE MG A1856
07AC7SOFTWAREGLY A:377 , TYR A:381 , ARG A:678BINDING SITE FOR RESIDUE 1PE A1857
08AC8SOFTWAREGLY A:720 , LYS A:722 , GLN A:725 , ASP A:771 , TYR A:804BINDING SITE FOR RESIDUE 1PE A1858
09AC9SOFTWAREALA A:369 , ILE A:370 , SER A:671 , LYS A:672 , PHE A:673 , TRP A:675 , PRO A:676 , ILE A:677 , ARG A:678 , 1PE A:1863BINDING SITE FOR RESIDUE 1PE A1859
10BC1SOFTWAREPHE A:647 , ASN A:650 , MET A:651 , HIS A:823 , HIS A:827BINDING SITE FOR RESIDUE 1PE A1860
11BC2SOFTWAREGLN A:362 , ASN A:841 , GLN A:843BINDING SITE FOR RESIDUE 1PE A1861
12BC3SOFTWAREARG A:829 , LEU A:834 , LEU A:844 , CYS A:845 , VAL A:847 , LEU A:849 , HOH A:2086BINDING SITE FOR RESIDUE 1PE A1862
13BC4SOFTWAREASN A:641 , ILE A:663 , THR A:667 , TRP A:675 , ILE A:677 , GLY A:679 , ILE A:680 , PRO A:681 , 1PE A:1859BINDING SITE FOR RESIDUE 1PE A1863
14BC5SOFTWAREHIS A:419 , ARG A:423 , LEU A:425 , SER A:426 , LEU A:427 , HIS A:629 , VAL A:630 , PRO A:631 , ILE A:632BINDING SITE FOR RESIDUE 1PE A1864
15BC6SOFTWAREPHE A:393 , HIS A:451 , ASP A:453 , LYS A:591 , GLN A:592BINDING SITE FOR RESIDUE 1PE A1865
16BC7SOFTWARESER A:412 , ASN A:415 , ALA A:416 , ILE A:632 , ARG A:633BINDING SITE FOR RESIDUE 1PE A1866
17BC8SOFTWARELYS A:367 , ASP A:371 , LYS A:373 , THR A:564 , LYS A:588BINDING SITE FOR RESIDUE 1PE A1867
18BC9SOFTWARELYS A:372 , ILE A:375 , SER A:376 , GLY A:589BINDING SITE FOR RESIDUE 1PE A1868

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:150 -Pro A:151

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2XZL)

(-) 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:756
 aligned with NAM7_YEAST | P30771 from UniProtKB/Swiss-Prot  Length:971

    Alignment length:791
                                    69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849 
           NAM7_YEAST    60 NSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSLHPDSDLGDTVLECYNCGRKNVFLLGFVSAKSEAVVVLLCRIPCAQTKNANWDTDQWQPLIEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDATINDIDAPEEQEAIPPLLLRYQDAYEYQRSYGPLIKLEADYDKQLKESQALEHISVSWSLALNNRHLASFTLSTFESNELKVAIGDEMILWYSGMQHPDWEGRGYIVRLPNSFQDTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQLCTVQLV 850
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains UPF1_Zn_bind-2xzlA03 A:60-208                                                                                                                        ----            ------------------------------------  --------------------         -------------------------------   ----------------------------------------------------------------------------------AAA_11-2xzlA01 A:408-609                                                                                                                                                                                  ------AAA_12-2xzlA02 A:616-813                                                                                                                                                                              ------------------------------------- Pfam domains
         Sec.struct. author .............eeee.....eee........hhhhhhhhhhh...eee.......................eeee.------.eeee........---.hhhhhee.................hhhhhh...hhhhhhhhhhhhh......------------.........hhhhhhhhhhhhhhhhhhhhhhhhh..--....eeeee.....eeeee.---------......eeeeee.......eeeeeeeee...---..eeeee..............eeeee...hhhhhhhhhhhhhhhhh....hhhhhhhhhh........................hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eee..hhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh........eeee.hhhhhhhhhhhhhhh....eeeeee..........hhhhhhh....hhhhhhhhh....ee..ee...hhhhhhhhhhhhh....ee......................eeeee.....ee......eehhhhhhhhhhhhhhhhhh..hhh.eeeee.hhhhhhhhhhhhhhhh..hhhhhhh.eeeehhhhh...eeeeeee.........hhhhhhhhhhhhhhh.eeeeeeeeehhhhhh.hhhhhhhhhhhhhhh.eeeee..eeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xzl A  60 NSCAYCGIDSAKCVIKCNSCKKWFCNTKNGTSSSHIVNHLVLSHHNVVSLHPDSDLGDTVLECYNCGRKNVFLLGFVS------VVLLCRIPCAQTK---WDTDQWQPLIEDRQLLSWVAEQPTEEEKLKARLITPSQISKLEAKWRSNKDAT------------IPPLLLRYQDAYEYQRSYGPLIKLEADYDKQLKESQ--EHISVSWSLALNNRHLASFT---------KVAIGDEMILWYSGMQHPDWEGRGYIVRLPN---DTFTLELKPSKTPPPTHLTTGFTAEFIWKGTSYDRMQDALKKFAIDKKSISGYLYYKILGHQVVDISFDVPLPKEFSIPNFAQLNSSQSNAVSHVLQRPLSLIQGPPGTGKTVTSATIVYHLSKIHKDRILVCAPSNVAVDHLAAKLRDLGLKVVRLTAKSREDVESSVSNLALHNLVGRGAKGELKNLLKLKDEVGELSASDTKRFVKLVRKTEAEILNKADVVCCTCVGAGDKRLDTKFRTVLIDESTQASEPECLIPIVKGAKQVILVGDHQQLGPVILERKAADAGLKQSLFERLISLGHVPIRLEVQYRMNPYLSEFPSNMFYEGSLQNGVTIEQRTVPNSKFPWPIRGIPMMFWANYGREEISANGTSFLNRIEAMNCERIITKLFRDGVKPEQIGVITPYEGQRAYILQYMQMNGSLDKDLYIKVEVASVDAFQGREKDYIILSCVRANEQQAIGFLRDPRRLNVGLTRAKYGLVILGNPRSLARNTLWNHLLIHFREKGCLVEGTLDNLQLCTVQLV 850
                                    69        79        89        99       109       119       129       | -    |  149      |  -|      169       179       189       199       209  |      -     | 229       239       249       259|  |   269       279  |      -  |    299       309       319  |   |329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679       689       699       709       719       729       739       749       759       769       779       789       799       809       819       829       839       849 
                                                                                                       137    144         156 160                                                 212          225                                260  |                282       292                           322 326                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                     263                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:DNA/RNA  Length:9
                                         
                 2xzl B   1 UUUUUUUUU   9
   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  (0, 0)

(no "SCOP Domain" information available for 2XZL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XZL)

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: P-loop_NTPase (1112)
(-)
Clan: no clan defined [family: UPF1_Zn_bind] (3)

(-) Gene Ontology  (23, 23)

Asymmetric Unit(hide GO term definitions)
Chain A   (NAM7_YEAST | P30771)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004004    ATP-dependent RNA helicase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction drives the unwinding of an RNA helix.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0004386    helicase activity    Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
    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: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.
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006310    DNA recombination    Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Intrachromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
    GO:0030466    chromatin silencing at silent mating-type cassette    Repression of transcription at silent mating-type loci by alteration of the structure of chromatin.
    GO:0008298    intracellular mRNA localization    Any process in which mRNA is transported to, or maintained in, a specific location within the cell.
    GO:0000956    nuclear-transcribed mRNA catabolic process    The chemical reactions and pathways resulting in the breakdown of nuclear-transcribed mRNAs in eukaryotic cells.
    GO:0070478    nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay    The chemical reactions and pathways resulting in the breakdown of the nuclear-transcribed mRNA transcript body of an mRNA in which an amino-acid codon has changed to a nonsense codon; occurs when the 3' end is not protected by a 3'-poly(A) tail; degradation proceeds in the 3' to 5' direction.
    GO:0000184    nuclear-transcribed mRNA catabolic process, nonsense-mediated decay    The nonsense-mediated decay pathway for nuclear-transcribed mRNAs degrades mRNAs in which an amino-acid codon has changed to a nonsense codon; this prevents the translation of such mRNAs into truncated, and potentially harmful, proteins.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0006449    regulation of translational termination    Any process that modulates the frequency, rate or extent of translational termination.
    GO:0006452    translational frameshifting    A mechanism whereby different proteins may result from a single mRNA molecule, due to a change in the parsing of three nucleotides per codon relative to an initiating AUG codon.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005844    polysome    A multiribosomal structure representing a linear array of ribosomes held together by messenger RNA. They represent the active complexes in cellular protein synthesis and are able to incorporate amino acids into polypeptides both in vivo and in vitro.

 Visualization

(-) Interactive Views

Asymmetric 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ALF  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:150 - Pro A:151   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  2xzl
    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
  NAM7_YEAST | P30771
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.6.4.13
    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
  NAM7_YEAST | P30771
    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 2XZL)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2XZL)