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(-) Description

Title :  CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF HNUP98
 
Authors :  Y. Sun, H. C. Guo
Date :  03 Jun 07  (Deposition) - 14 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Nup98, Nucleoporin, Autoproteolysis, Protein Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Sun, H. C. Guo
Structural Constraints On Autoprocessing Of The Human Nucleoporin Nup98.
Protein Sci. V. 17 494 2008
PubMed-ID: 18287282  |  Reference-DOI: 10.1110/PS.073311808
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEAR PORE COMPLEX PROTEIN NUP98
    ChainsA, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-21A
    Expression System StrainBL21(DE3)
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN, RESIDUES 729-880
    GeneNUP98
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymNUCLEOPORIN NUP98, 98 KDA NUCLEOPORIN
 
Molecule 2 - NUCLEAR PORE COMPLEX PROTEIN NUP96
    ChainsB, D
    EngineeredYES
    FragmentRESIDUES 881-887
    Other DetailsTHIS SEQUENCE IS NATURALLY PRESENT IN HUMANS
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2Q5Y)

(-) Sites  (0, 0)

(no "Site" information available for 2Q5Y)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Q5Y)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:727 -Pro A:728
2Ile C:727 -Pro C:728

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Q5Y)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUP_CPS51434 NUP C-terminal domain profile.NUP98_HUMAN738-880
 
  2A:721-863
C:721-863
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUP_CPS51434 NUP C-terminal domain profile.NUP98_HUMAN738-880
 
  1A:721-863
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUP_CPS51434 NUP C-terminal domain profile.NUP98_HUMAN738-880
 
  1-
C:721-863

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003591711bENSE00001266767chr11:3818892-3818630263NUP98_HUMAN-00--
1.2ENST000003591712ENSE00001331927chr11:3803375-3803272104NUP98_HUMAN1-26260--
1.3ENST000003591713ENSE00001266763chr11:3800487-3800386102NUP98_HUMAN26-60350--
1.4bENST000003591714bENSE00001266760chr11:3800279-3800103177NUP98_HUMAN60-119600--
1.5bENST000003591715bENSE00001057882chr11:3797251-3797112140NUP98_HUMAN119-165470--
1.6ENST000003591716ENSE00000891053chr11:3794969-3794862108NUP98_HUMAN166-201360--
1.7ENST000003591717ENSE00000891055chr11:3793158-3792978181NUP98_HUMAN202-262610--
1.8aENST000003591718aENSE00001112039chr11:3789974-3789811164NUP98_HUMAN262-316550--
1.9aENST000003591719aENSE00000891059chr11:3784269-3784132138NUP98_HUMAN317-362460--
1.10bENST0000035917110bENSE00001485193chr11:3781856-3781718139NUP98_HUMAN363-409470--
1.11ENST0000035917111ENSE00001057883chr11:3774638-377454693NUP98_HUMAN409-440320--
1.12aENST0000035917112aENSE00001057881chr11:3765879-3765739141NUP98_HUMAN440-487480--
1.13ENST0000035917113ENSE00001057868chr11:3756554-3756421134NUP98_HUMAN487-531450--
1.14aENST0000035917114aENSE00001057874chr11:3752808-3752621188NUP98_HUMAN532-594630--
1.15ENST0000035917115ENSE00002140746chr11:3746449-3746333117NUP98_HUMAN594-633400--
1.16ENST0000035917116ENSE00001057846chr11:3744685-3744387299NUP98_HUMAN633-7331012A:712-716
C:712-716
5
5
1.17bENST0000035917117bENSE00001057869chr11:3742055-3741942114NUP98_HUMAN733-771392A:716-754
C:716-754
39
39
1.18bENST0000035917118bENSE00001057877chr11:3740780-3740642139NUP98_HUMAN771-817472A:754-800
C:754-800 (gaps)
47
47
1.19ENST0000035917119ENSE00001057851chr11:3735225-3735048178NUP98_HUMAN817-876602A:800-859
C:800-859
60
60
1.20aENST0000035917120aENSE00001057857chr11:3733958-3733794165NUP98_HUMAN877-931552A:860-863
C:860-863
4
4
1.21aENST0000035917121aENSE00000988546chr11:3727857-3727675183NUP98_HUMAN932-992610--
1.22ENST0000035917122ENSE00001266871chr11:3726586-3726430157NUP98_HUMAN993-1045530--
1.23bENST0000035917123bENSE00001350501chr11:3724122-3723693430NUP98_HUMAN1045-11881440--
1.24aENST0000035917124aENSE00001266800chr11:3722069-3721840230NUP98_HUMAN1188-1265780--
1.25aENST0000035917125aENSE00000891085chr11:3720578-3720312267NUP98_HUMAN1265-1354900--
1.27cENST0000035917127cENSE00001057884chr11:3716836-3716679158NUP98_HUMAN1354-1406530--
1.28aENST0000035917128aENSE00001266845chr11:3714605-3714462144NUP98_HUMAN1407-1454480--
1.29ENST0000035917129ENSE00001057852chr11:3712719-3712577143NUP98_HUMAN1455-1502480--
1.30bENST0000035917130bENSE00001120869chr11:3707424-3707203222NUP98_HUMAN1502-1576750--
1.31ENST0000035917131ENSE00001300941chr11:3704671-3704430242NUP98_HUMAN1576-1657820--
1.32dENST0000035917132dENSE00001777516chr11:3700938-3700780159NUP98_HUMAN1657-1710540--
1.33ENST0000035917133ENSE00001623583chr11:3699832-369981419NUP98_HUMAN1710-171670--
1.34cENST0000035917134cENSE00001790157chr11:3697847-369780543NUP98_HUMAN1716-1729140--

(-) 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:152
 aligned with NUP98_HUMAN | P52948 from UniProtKB/Swiss-Prot  Length:1817

    Alignment length:152
                                   738       748       758       768       778       788       798       808       818       828       838       848       858       868       878  
          NUP98_HUMAN   729 MHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF 880
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2q5yA00 A:712-863 c-terminal autoproteolytic domain of nucleoporin nup98                                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeee.hhhhhhhh.......eeeeeeeee...eeeeeeeeee....hhhhheeee..eeee..hhhhh..........eeeee...............hhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------NUP_C  PDB: A:721-863 UniProt: 738-880                                                                                                          PROSITE
           Transcript 1 (1) 1.16 -------------------------------------Exon 1.18b  PDB: A:754-800 UniProt: 771-817    -----------------------------------------------------------1.20 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.17b  PDB: A:716-754             ---------------------------------------------Exon 1.19  PDB: A:800-859 UniProt: 817-876                  ---- Transcript 1 (2)
                 2q5y A 712 MHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF 863
                                   721       731       741       751       761       771       781       791       801       811       821       831       841       851       861  

Chain B from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2q5y B 866 YGL 868

Chain C from PDB  Type:PROTEIN  Length:148
 aligned with NUP98_HUMAN | P52948 from UniProtKB/Swiss-Prot  Length:1817

    Alignment length:152
                                   738       748       758       768       778       788       798       808       818       828       838       848       858       868       878  
          NUP98_HUMAN   729 MHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF 880
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Nucleoporin2-2q5yC01 C:723-863                                                                                                                Pfam domains (1)
           Pfam domains (2) -----------Nucleoporin2-2q5yC02 C:723-863                                                                                                                Pfam domains (2)
         Sec.struct. author ............eeee.hhhhhhhh.......eeeeeeeee...eeeeeeeeee....hhhhheeee..eeee..----...........eeeee...............hhhhhhhhhhhhhhhhhhhhh..eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------NUP_C  PDB: C:721-863 UniProt: 738-880                                                                                                          PROSITE
           Transcript 1 (1) 1.16 -------------------------------------Exon 1.18b  PDB: C:754-800 (gaps)              -----------------------------------------------------------1.20 Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.17b  PDB: C:716-754             ---------------------------------------------Exon 1.19  PDB: C:800-859 UniProt: 817-876                  ---- Transcript 1 (2)
                 2q5y C 712 MHPAGIILTKVGYYTIPSMDDLAKITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIVHIRRKEVVVYL----KPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRLEAVSRKQGAQFKEYRPETGSWVFKVSHF 863
                                   721       731       741       751       761       771       781    |  791       801       811       821       831       841       851       861  
                                                                                                    786  791                                                                        

Chain D from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2q5y D 866 YGL 868

   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 2Q5Y)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (NUP98_HUMAN | P52948)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008139    nuclear localization sequence binding    Interacting selectively and non-covalently with a nuclear localization sequence, a specific peptide sequence that acts as a signal to localize the protein within the nucleus.
    GO:0005487    nucleocytoplasmic transporter activity    Enables the directed movement of substances between the nucleus and the cytoplasm of a cell.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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:0017056    structural constituent of nuclear pore    The action of a molecule that contributes to the structural integrity of the nuclear pore complex.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0006405    RNA export from nucleus    The directed movement of RNA from the nucleus to the cytoplasm.
    GO:0031047    gene silencing by RNA    Any process in which RNA molecules inactivate expression of target genes.
    GO:0075733    intracellular transport of virus    The directed movement of a virus, or part of a virus, within the host cell.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007077    mitotic nuclear envelope disassembly    The cell cycle process in which the controlled breakdown of the nuclear envelope during mitotic cell division occurs.
    GO:0051292    nuclear pore complex assembly    The aggregation, arrangement and bonding together of a set of components to form a nuclear pore complex.
    GO:0006999    nuclear pore organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the nuclear pore.
    GO:0006913    nucleocytoplasmic transport    The directed movement of molecules between the nucleus and the cytoplasm.
    GO:0000059    obsolete protein import into nucleus, docking    OBSOLETE. A protein complex assembly process that contributes to protein import into the nucleus, and that results in the association of a cargo protein, a carrier protein such as an importin alpha/beta heterodimer, and a nucleoporin located at the periphery of the nuclear pore complex.
    GO:0000973    posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery    The chromosome organization process in which the DNA sequence containing a gene transcribed by RNA polymerase II is maintained in a specific location at the nuclear periphery even after transcription has been repressed.
    GO:0016925    protein sumoylation    The process in which a SUMO protein (small ubiquitin-related modifier) is conjugated to a target protein via an isopeptide bond between the carboxyl terminus of SUMO with an epsilon-amino group of a lysine residue of the target protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0010827    regulation of glucose transport    Any process that modulates the frequency, rate or extent of glucose transport. Glucose transport is the directed movement of the hexose monosaccharide glucose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007062    sister chromatid cohesion    The cell cycle process in which the sister chromatids of a replicated chromosome become tethered to each other.
    GO:0006409    tRNA export from nucleus    The directed movement of tRNA from the nucleus to the cytoplasm.
    GO:0034398    telomere tethering at nuclear periphery    The process in which a telomere is maintained in a specific location at the nuclear periphery.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
    GO:0019083    viral transcription    The process by which a viral genome, or part of a viral genome, is transcribed within the host cell.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0042405    nuclear inclusion body    An intranuclear focus at which aggregated proteins have been sequestered.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0034399    nuclear periphery    The portion of the nuclear lumen proximal to the inner nuclear membrane.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    GO:0044614    nuclear pore cytoplasmic filaments    Filamentous extensions on cytoplasmic face of the nuclear pore complex (NPC). In S. cerevisiae, Nup159p, Nup82p, and Nup42p contribute to the cytoplasmic filaments. In vertebrates, Nup358 is a major component.
    GO:0044615    nuclear pore nuclear basket    A filamentous, cage-like assembly on the nuclear face of the nuclear pore complex (NPC). In S. cerevisiae, Mlp1p and Mlp2p are two major components of the NPC nuclear basket. In vertebrates, Tpr is a major component.
    GO:0031080    nuclear pore outer ring    A subcomplex of the nuclear pore complex (NPC) that forms the outer rings of the core scaffold, a lattice-like structure that gives the NPC its shape and strength. In S. cerevisiae, the two outer rings each contain multiple copies of the following proteins: Nup133p, Nup120p, Nup145Cp, Nup85p, Nup84p, Seh1p, and Sec13p. In vertebrates, the two outer rings each contain multiple copies of the following proteins: Nup133, Nup160, Nup96, Nup75, Nup107, Seh1, Sec13, Nup43, Nup37, and ALADIN. Components are arranged in 8-fold symmetrical 'spokes' around the central transport channel. A single 'spoke', can be isolated and is sometimes referred to as the Nup84 complex (S. cerevisiae) or the Nup107-160 complex (vertebrates).
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NUP98_HUMAN | P529481ko6 2q5x 3mmy 4owr 5a9q

(-) Related Entries Specified in the PDB File

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