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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN PIM2 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1
 
Authors :  S. Russo, J. E. Debreczeni, A. Amos, A. N. Bullock, O. Fedorov, F. Niesen F. Sobott, A. Turnbull, A. C. W. Pike, E. Ugochukwu, E. Papagrigoriou, G. Bunkoczi, F. Gorrec, A. Edwards, C. Arrowsmith, J. Weigelt, M. Sundstrom, F. Von Delft, S. Knapp
Date :  30 Jun 06  (Deposition) - 02 Aug 06  (Release) - 03 Nov 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Nucleotide-Binding, Serine/Threonine-Protein Kinase, Pim2, Kinase, Cancer, Leukemia, Transferase, Atp-Binding, Proto- Oncogene, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. N. Bullock, S. Russo, A. Amos, N. Pagano, H. Bregman, J. E. Debreczeni, W. H. Lee, F. Von Delft, E. Meggers, S. Knapp
Crystal Structure Of The Pim2 Kinase In Complex With An Organoruthenium Inhibitor.
Plos One V. 4 E7112 2009
PubMed-ID: 19841674  |  Reference-DOI: 10.1371/JOURNAL.PONE.0007112

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PIM-2
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Cell LineBL21(DE3) STAR
    Expression System Taxid562
    Expression System VectorPLIC-SGC1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUMAN PIM2, PIM-2H

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1HB12Ligand/IonRUTHENIUM-PYRIDOCARBAZOLE-1
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1HB11Ligand/IonRUTHENIUM-PYRIDOCARBAZOLE-1
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1HB11Ligand/IonRUTHENIUM-PYRIDOCARBAZOLE-1

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:39 , PHE A:43 , VAL A:46 , ILE A:100 , LEU A:116 , GLU A:117 , ARG A:118 , ASP A:124 , GLU A:167 , LEU A:170 , ILE A:181 , ASP A:182BINDING SITE FOR RESIDUE HB1 A1289
2AC2SOFTWAREGLY B:39 , PHE B:43 , VAL B:46 , LEU B:116 , GLU B:117 , ARG B:118 , GLU B:167 , LEU B:170 , ILE B:181 , ASP B:182BINDING SITE FOR RESIDUE HB1 B1288

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:120 -Pro A:121
2Leu B:120 -Pro B:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041008G138DPIM2_HUMANPolymorphism35044770A/BG138D
2UniProtVAR_041009I280VPIM2_HUMANPolymorphism35208542A/BI280V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041008G138DPIM2_HUMANPolymorphism35044770AG138D
2UniProtVAR_041009I280VPIM2_HUMANPolymorphism35208542AI280V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041008G138DPIM2_HUMANPolymorphism35044770BG138D
2UniProtVAR_041009I280VPIM2_HUMANPolymorphism35208542BI280V

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PIM2_HUMAN38-61
 
  2A:38-61
B:38-61
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PIM2_HUMAN159-171
 
  2A:159-171
B:159-171
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PIM2_HUMAN38-61
 
  1A:38-61
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PIM2_HUMAN159-171
 
  1A:159-171
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PIM2_HUMAN38-61
 
  1-
B:38-61
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PIM2_HUMAN159-171
 
  1-
B:159-171

(-) Exons   (5, 10)

Asymmetric Unit (5, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003765091ENSE00001470752X:48776301-48776051251PIM2_HUMAN1-21210--
1.2ENST000003765092ENSE00000670819X:48775922-48775813110PIM2_HUMAN21-57372A:32-57
B:22-57
26
36
1.3ENST000003765093ENSE00000670821X:48775108-4877505851PIM2_HUMAN58-74172A:58-69
B:58-65
12
8
1.4bENST000003765094bENSE00000670823X:48772669-48772297373PIM2_HUMAN75-1991252A:78-199 (gaps)
B:79-199 (gaps)
122
121
1.5cENST000003765095cENSE00000670825X:48771848-48771672177PIM2_HUMAN199-258602A:199-258
B:199-258
60
60
1.6bENST000003765096bENSE00001470750X:48771571-487704591113PIM2_HUMAN258-311542A:258-288
B:258-287
31
30

(-) 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:244
 aligned with PIM2_HUMAN | Q9P1W9 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:257
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       
           PIM2_HUMAN    32 YRLGPLLGKGGFGTVFAGHRLTDRLQVAIKVIPRNRVLGWSPLSDSVTCPLEVALLWKVGAGGGHPGVIRLLDWFETQEGFMLVLERPLPAQDLFDYITEKGPLGEGPSRCFFGQVVAAIQHCHSRGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFERDQEILEAELHFPAHVSPDCCALIRRCLAPKPSSRPSLEEILLDPWMQT 288
               SCOP domains d2iwia_ A: automated matches                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2iwiA01 A:32-120 Phosphorylase Kinase;         domain 1                                  2iwiA02 A:121-288 Transferase(Phosphotransferase) domain 1                                                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..eeeeeee......eeeeee.......--------...hhhhhhhhhhhh.........eeee.-----.eeeee....eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eeee....eeee......ee................hhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhh........hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------V-------- SAPs(SNPs)
                    PROSITE ------PROTEIN_KINASE_ATP      -------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:32-57    Exon 1.3         Exon 1.4b  PDB: A:78-199 (gaps) UniProt: 75-199 [INCOMPLETE]                                                                 ----------------------------------------------------------Exon 1.6b  PDB: A:258-288       Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5c  PDB: A:199-258 UniProt: 199-258                  ------------------------------ Transcript 1 (2)
                 2iwi A  32 YRLGPLLGKGGFGTVFAGHRLTDRLQVAIKVIPRNRVL--------VTCPLEVALLWKVGAGGGHPGVIRLLDWF-----FMLVLERPLPAQDLFDYITEKGPLGEGPSRCFFGQVVAAIQHCHSRGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFERDQEILEAELHFPAHVSPDCCALIRRCLAPKPSSRPSLEEILLDPWMQT 288
                                    41        51        61       | -      | 81        91       101    |    -|      121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       
                                                                69       78                         106   112                                                                                                                                                                                

Chain B from PDB  Type:PROTEIN  Length:249
 aligned with PIM2_HUMAN | Q9P1W9 from UniProtKB/Swiss-Prot  Length:311

    Alignment length:266
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281      
           PIM2_HUMAN    22 GKDREAFEAEYRLGPLLGKGGFGTVFAGHRLTDRLQVAIKVIPRNRVLGWSPLSDSVTCPLEVALLWKVGAGGGHPGVIRLLDWFETQEGFMLVLERPLPAQDLFDYITEKGPLGEGPSRCFFGQVVAAIQHCHSRGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFERDQEILEAELHFPAHVSPDCCALIRRCLAPKPSSRPSLEEILLDPWMQ 287
               SCOP domains d2iwib_ B: automated matches                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2iwiB01 B:22-120 Phosphorylase Kinase; domai             n 1                                       2iwiB02 B:121-287 Transferase(Phosphotransferase) domain 1                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.eeeeeeeeee..eeeeeeee....eeeeeee...-------------..hhhhhhhhhhhh.........eeeee.----.eeeee....eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhee....hhh.eeee....eeee......ee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhh........hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------D---------------------------------------------------------------------------------------------------------------------------------------------V------- SAPs(SNPs)
                    PROSITE ----------------PROTEIN_KINASE_ATP      -------------------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2  PDB: B:22-57 [INCOMPLETE] Exon 1.3         Exon 1.4b  PDB: B:79-199 (gaps) UniProt: 75-199 [INCOMPLETE]                                                                 ----------------------------------------------------------Exon 1.6b  PDB: B:258-287      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.5c  PDB: B:199-258 UniProt: 199-258                  ----------------------------- Transcript 1 (2)
                 2iwi B  22 GKDREAFEAEYRLGPLLGKGGFGTVFAGHRLTDRLQVAIKVIPR-------------TCPLEVALLWKVGAGGGHPGVIRLLDWFE----FMLVLERPLPAQDLFDYITEKGPLGEGPSRCFFGQVVAAIQHCHSRGVVHRDIKDENILIDLRRGCAKLIDFGSGALLHDEPYTDFDGTRVYSPPEWISRHQYHALPATVWSLGILLYDMVCGDIPFERDQEILEAELHFPAHVSPDCCALIRRCLAPKPSSRPSLEEILLDPWMQ 287
                                    31        41        51        61   |     -       |81        91       101     |   -|      121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281      
                                                                      65            79                         107  112                                                                                                                                                                               

   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 Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2IWI)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PIM2_HUMAN | Q9P1W9)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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: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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007140    male meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the male germline.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0043123    positive regulation of I-kappaB kinase/NF-kappaB signaling    Any process that activates or increases the frequency, rate or extent of I-kappaB kinase/NF-kappaB signaling.
    GO:0010508    positive regulation of autophagy    Any process that activates, maintains or increases the rate of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0009615    response to virus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a virus.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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        PIM2_HUMAN | Q9P1W94x7q

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