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(-) Description

Title :  HUMAN INOSITOL (1,4,5)-TRISPHOSPHATE 3-KINASE SUBSTITUTED WITH SELENOMETHIONINE
 
Authors :  B. Gonzalez, M. J. Schell, R. F. Irvine, R. L. Williams
Date :  01 Jul 04  (Deposition) - 09 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Inositol Phosphate Kinase, Transferase, Calmodulin-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Gonzalez, M. J. Schell, A. J. Letcher, D. B. Veprintsev, R. F. Irvine R. L. Williams
Structure Of A Human Inositol 1, 4, 5-Trisphosphate 3-Kinase; Substrate Binding Reveals Why It Is Not A Phosphoinositide 3-Kinase
Mol. Cell V. 15 689 2004
PubMed-ID: 15350214  |  Reference-DOI: 10.1016/J.MOLCEL.2004.08.004

(-) Compounds

Molecule 1 - INOSITOL-TRISPHOSPHATE 3-KINASE A
    ChainsA, B
    EC Number2.1.7.127
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainB834
    Expression System Taxid562
    Expression System VariantDE3
    Expression System VectorPOPTG
    FragmentCATALYTIC DOMAIN, RESIDUES 186-461
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymINOSITOL 1,4,5-TRISPHOSPHATE 3-KINASE, IP3-3K

 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  (2, 16)

Asymmetric Unit (2, 16)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 7)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:264 , LYS A:312 , LYS A:419 , HOH A:2026 , HOH A:2125BINDING SITE FOR RESIDUE SO4 A1462
2AC2SOFTWAREARG A:285 , MSE A:288 , LYS A:312BINDING SITE FOR RESIDUE SO4 A1463
3AC3SOFTWARETYR A:315 , ARG A:319 , HOH A:2144 , HOH A:2145BINDING SITE FOR RESIDUE SO4 A1464
4AC4SOFTWARELYS B:291 , TYR B:315 , ARG B:319BINDING SITE FOR RESIDUE SO4 B1462

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W2F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1W2F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W2F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1W2F)

(-) Exons   (6, 12)

Asymmetric Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002603862aENSE00001206292chr15:41786059-41786614556IP3KA_HUMAN1-1631630--
1.3bENST000002603863bENSE00000931025chr15:41793661-4179375797IP3KA_HUMAN164-196332A:186-196
B:186-192
11
7
1.4aENST000002603864aENSE00000931026chr15:41793833-41794049217IP3KA_HUMAN196-268732A:196-268
B:197-268
73
72
1.5ENST000002603865ENSE00000931027chr15:41794195-41794399205IP3KA_HUMAN268-336692A:268-336
B:268-336
69
69
1.6bENST000002603866bENSE00000931028chr15:41794600-41794701102IP3KA_HUMAN337-370342A:337-370
B:337-370
34
34
1.7ENST000002603867ENSE00000931029chr15:41794986-4179505772IP3KA_HUMAN371-394242A:371-394
B:371-394
24
24
1.8bENST000002603868bENSE00000931030chr15:41795161-41795749589IP3KA_HUMAN395-461672A:395-461
B:395-461
67
67

(-) 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:276
 aligned with IP3KA_HUMAN | P23677 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:276
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455      
          IP3KA_HUMAN   186 YAWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
               SCOP domains d1w2fa_ A: Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhh.....ee.....eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.........eeeeeee.....hhhhhhhhhhh..eehhhhhhhhhhh....hhhhhhhh.eehhhhhhhhhhhhhhhhhheeeeeee.....ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeeee.....eeeeee...eeee....................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  -----------------------------------------------------------------------Exon 1.5  PDB: A:268-336 UniProt: 268-336                            Exon 1.6b  PDB: A:337-370         Exon 1.7  PDB: A:371-394Exon 1.8b  PDB: A:395-461 UniProt: 395-461                          Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.4a  PDB: A:196-268 UniProt: 196-268                               ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1w2f A 186 mSWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLmADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKmGVRTYLEEELTKARERPKLRKDmYKKmLAVDPEAPTEEEHAQRAVTKPRYmQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
                            |      195       205       215       225       235       245       255       265       275       285  |   |295       305       315|      325       335       345       355       365       375       385       395       405       415       425       435       445       455      
                            |                                  223-MSE                                   265-MSE                288-MSE                     316-MSE                                                                                                                                             
                          186-MSE                                                                                                   292-MSE                                                                                                                                                                     

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with IP3KA_HUMAN | P23677 from UniProtKB/Swiss-Prot  Length:461

    Alignment length:276
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455      
          IP3KA_HUMAN   186 YAWVQLAGHTGSFKAAGTSGLILKRCSEPERYCLARLMADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKMGVRTYLEEELTKARERPKLRKDMYKKMLAVDPEAPTEEEHAQRAVTKPRYMQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
               SCOP domains d1w2fb_     B: Inositol 1,4,5-trisphosphate 3-kinase A, IP3K A                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------------------------------------------------IPK-1w2fB01 B:245-456                                                                                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------IPK-1w2fB02 B:245-456                                                                                                                                                                                               ----- Pfam domains (2)
         Sec.struct. author .hhhhhh----.eee.....eeeee.hhhhhhhhhhhhhhhhhhhh..eeeeeee..eeeeeee.........eeeeeee.....hhhhhhhhhhh..eehhhhhhhhhhh....hhhhhhhh.eehhhhhhhhhhhhhhhhhheeeeeee.....ee.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhheeee..eeeeee.....eeeeee...eeee....................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.3b  -----------------------------------------------------------------------Exon 1.5  PDB: B:268-336 UniProt: 268-336                            Exon 1.6b  PDB: B:337-370         Exon 1.7  PDB: B:371-394Exon 1.8b  PDB: B:395-461 UniProt: 395-461                          Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.4a  PDB: B:197-268 UniProt: 196-268 [INCOMPLETE]                  ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 1w2f B 186 mSWVQLA----SFKAAGTSGLILKRCSEPERYCLARLmADALRGCVPAFHGVVERDGESYLQLQDLLDGFDGPCVLDCKmGVRTYLEEELTKARERPKLRKDmYKKmLAVDPEAPTEEEHAQRAVTKPRYmQWREGISSSTTLGFRIEGIKKADGSCSTDFKTTRSREQVLRVFEEFVQGDEEVLRRYLNRLQQIRDTLEVSEFFRRHEVIGSSLLFVHDHCHRAGVWLIDFGKTTPLPDGQILDHRRPWEEGNREDGYLLGLDNLIGILASLAER 461
                            |     |  - |     205       215       225       235       245       255       265       275       285  |   |295       305       315|      325       335       345       355       365       375       385       395       405       415       425       435       445       455      
                          186-MSE92  197                       223-MSE                                   265-MSE                288-MSE                     316-MSE                                                                                                                                             
                                                                                                                                    292-MSE                                                                                                                                                                     

   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  (0, 0)

(no "CATH Domain" information available for 1W2F)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: IPK (3)
1aIPK-1w2fB01B:245-456
1bIPK-1w2fB02B:245-456

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IP3KA_HUMAN | P23677)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0048365    Rac GTPase binding    Interacting selectively and non-covalently with Rac protein, any member of the Rac subfamily of the Ras superfamily of monomeric GTPases.
    GO:0005516    calmodulin binding    Interacting selectively and non-covalently with calmodulin, a calcium-binding protein with many roles, both in the calcium-bound and calcium-free states.
    GO:0004683    calmodulin-dependent protein kinase activity    Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; and ATP + a protein threonine = ADP + protein threonine phosphate. These reactions require the presence of calcium-bound calmodulin.
    GO:0008440    inositol-1,4,5-trisphosphate 3-kinase activity    Catalysis of the reaction: 1D-myo-inositol 1,4,5-trisphosphate + ATP = 1D-myo-inositol 1,3,4,5-tetrakisphosphate + ADP + 2 H(+).
    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: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:0030036    actin cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0097062    dendritic spine maintenance    The organization process that preserves a dendritic spine in a stable functional or structural state. A dendritic spine is a specialized protrusion from a neuronal dendrite and is involved in synaptic transmission.
    GO:0006020    inositol metabolic process    The chemical reactions and pathways involving inositol, 1,2,3,4,5,6-cyclohexanehexol, a growth factor for animals and microorganisms.
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
    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:0061003    positive regulation of dendritic spine morphogenesis    Any process that increases the rate, frequency, or extent of dendritic spine morphogenesis, the process in which the anatomical structures of a dendritic spine are generated and organized. A dendritic spine is a protrusion from a dendrite and a specialized subcellular compartment involved in synaptic transmission.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0048167    regulation of synaptic plasticity    A process that modulates synaptic plasticity, the ability of synapses to change as circumstances require. They may alter function, such as increasing or decreasing their sensitivity, or they may increase or decrease in actual numbers.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving 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:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.

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 Related Entries

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

UniProtKB/Swiss-Prot
        IP3KA_HUMAN | P236771w2c 1w2d 4upu

(-) Related Entries Specified in the PDB File

1w2c HUMAN INOSITOL (1,4,5) TRISPHOSPHATE 3- KINASE COMPLEXED WITH MN2+/AMPPNP/INS(1,4,5)P3
1w2d HUMAN INOSITOL (1,4,5)-TRISPHOSPHATE 3- KINASE COMPLEXED WITH MN2+/ADP/INS(1,3,4,5)P4