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(-) Description

Title :  STRUCTURE OF PCDK2/CYCLINA BOUND TO ADP AND 2 MAGNESIUM IONS
 
Authors :  D. M. Jacobsen, Z. -Q. Bao, P. J. O'Brien, C. L. Brooks, M. A. Young
Date :  27 Nov 12  (Deposition) - 26 Dec 12  (Release) - 26 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Adp And Magnesium Binding, T160 Phosphorylation, Transferase-Cell Cycle Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. Jacobsen, Z. -Q. Bao, P. J. O'Brien, C. L. Brooks, M. A. Young
Price To Be Paid For Two-Metal Catalysis: Magnesium Ions That Accelerate Chemistry Unavoidably Limit Product Release From A Protein Kinase
J. Am. Chem. Soc. V. 134 15357 2012
PubMed-ID: 22891849

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 2
    Chains: A, C
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: CDK2, CDKN2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 2, P33 PROTEIN KINASE
 
Molecule 2 - CYCLIN-A2
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 105-421
    Gene: CCNA, CCNA2, CYCA
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: CYCLIN-A

 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  (5, 19)

Asymmetric Unit (5, 19)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3GOL9Ligand/IonGLYCEROL
4MG4Ligand/IonMAGNESIUM ION
5TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 7)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL5Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4MG-1Ligand/IonMAGNESIUM ION
5TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:10 , ALA A:31 , LYS A:33 , GLU A:81 , LEU A:83 , ASP A:86 , LYS A:89 , GLN A:131 , ASN A:132 , LEU A:134 , ASP A:145 , MG A:302 , MG A:303 , GOL A:306 , HOH A:401 , HOH A:404 , HOH A:409 , HOH A:435 , HOH A:440 , HOH A:460BINDING SITE FOR RESIDUE ADP A 301
02AC2SOFTWAREASN A:132 , ASP A:145 , ADP A:301 , HOH A:401 , HOH A:402BINDING SITE FOR RESIDUE MG A 302
03AC3SOFTWAREASP A:145 , ADP A:301 , HOH A:403 , HOH A:404 , HOH A:413BINDING SITE FOR RESIDUE MG A 303
04AC4SOFTWAREILE A:209 , ASP A:210 , PHE A:213 , ARG A:217 , GLU D:224 , TYR D:225 , GLU D:277BINDING SITE FOR RESIDUE GOL A 304
05AC5SOFTWAREPHE A:4 , ASN A:23 , GLU A:28 , VAL A:30 , ASP A:68 , HOH A:405 , HOH A:513BINDING SITE FOR RESIDUE GOL A 305
06AC6SOFTWAREASP A:86 , LYS A:88 , LYS A:89 , ADP A:301BINDING SITE FOR RESIDUE GOL A 306
07AC7SOFTWAREGLN A:131BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREGLU B:224 , TYR B:225 , GLU B:277 , ILE C:209 , ASP C:210 , PHE C:213 , ARG C:217BINDING SITE FOR RESIDUE GOL B 501
09AC9SOFTWARETYR B:199 , ARG B:202 , GLN B:203 , LEU B:243 , SER B:244 , MET B:246 , SER B:247BINDING SITE FOR RESIDUE GOL B 502
10BC1SOFTWAREILE C:10 , ALA C:31 , LYS C:33 , GLU C:81 , PHE C:82 , LEU C:83 , ASP C:86 , LYS C:89 , GLN C:131 , ASN C:132 , LEU C:134 , ASP C:145 , MG C:302 , MG C:303 , HOH C:401 , HOH C:402 , HOH C:404 , HOH C:415 , HOH C:433 , HOH C:446 , HOH C:452BINDING SITE FOR RESIDUE ADP C 301
11BC2SOFTWAREASN C:132 , ASP C:145 , ADP C:301 , HOH C:401 , HOH C:402BINDING SITE FOR RESIDUE MG C 302
12BC3SOFTWAREASP C:145 , ADP C:301 , HOH C:403 , HOH C:404 , HOH C:406 , HOH C:410BINDING SITE FOR RESIDUE MG C 303
13BC4SOFTWAREPHE C:4 , ASN C:23 , GLU C:28 , ASP C:68 , HOH C:408BINDING SITE FOR RESIDUE GOL C 304
14BC5SOFTWAREPRO C:130 , GLN C:131BINDING SITE FOR RESIDUE CL C 305
15BC6SOFTWAREPRO A:228 , GLN D:370 , SER D:371 , PRO D:373 , HOH D:647BINDING SITE FOR RESIDUE GOL D 501
16BC7SOFTWARETHR D:184 , ARG D:187 , GLN D:379 , HOH D:753BINDING SITE FOR RESIDUE GOL D 502
17BC8SOFTWARETYR D:199 , ARG D:202 , GLN D:203 , LEU D:243 , SER D:244 , SER D:247BINDING SITE FOR RESIDUE GOL D 503

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I3Z)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Val A:154 -Pro A:155
2Gln B:323 -Pro B:324
3Asp B:345 -Pro B:346
4Val C:154 -Pro C:155
5Gln D:323 -Pro D:324
6Asp D:345 -Pro D:346

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I3Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I3Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4I3Z)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4i3za_ A: Cyclin-dependent PK, CDK2                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...eeeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeeee...eeeeeee...eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3z A   1 MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYtHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHL 296
                                    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      
                                                                                                                                                                                         160-TPO                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4i3zb1 B:175-309 automated matches                                                                                                    d4i3zb2 B:310-431 automated matches                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3z B 175 VPDYQEDIHTYLREMEVKCKPKVGYMKRQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYSKKQVLRMEHLVLKVLAFDLAAPTVNQFLTQYFLHLQPANCKVESLAMFLGELSLIDADPYLKYLPSLIAGAAFHLALYTVTGQSWPESLAQQTGYTLESLKPCLVDLHQTYLKAPQHAQQSIREKYKHSKYHSVSLLNPPETLS 431
                                   184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       


Chain C from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4i3zc_ C: Cyclin-dependent PK, CDK2                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee...eeeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeeee...eeeeeee...eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh........hhhhh.............hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3z C   1 MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYtHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHL 296
                                    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      
                                                                                                                                                                                         160-TPO                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains d4i3zd1 D:175-309 automated matches                                                                                                    d4i3zd2 D:310-431 automated matches                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh....hhhhhhhhh....hhhhhhhhhhhhhhhhh......hhhhhhhhhhh.....hhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i3z D 175 VPDYQEDIHTYLREMEVKCKPKVGYMKRQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYSKKQVLRMEHLVLKVLAFDLAAPTVNQFLTQYFLHLQPANCKVESLAMFLGELSLIDADPYLKYLPSLIAGAAFHLALYTVTGQSWPESLAQQTGYTLESLKPCLVDLHQTYLKAPQHAQQSIREKYKHSKYHSVSLLNPPETLS 431
                                   184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424
   Legend:   → Mismatch (orange background)
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    → 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  (2, 6)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I3Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I3Z)

(-) Gene Ontology  (82, 93)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CCNA2_MOUSE | P51943: 3qhr 3qhw 4ii5
        CDK2_HUMAN | P24941: 1aq1 1b38 1b39 1buh 1ckp 1di8 1dm2 1e1v 1e1x 1e9h 1f5q 1fin 1fq1 1fvt 1fvv 1g5s 1gih 1gii 1gij 1gy3 1gz8 1h00 1h01 1h07 1h08 1h0v 1h0w 1h1p 1h1q 1h1r 1h1s 1h24 1h25 1h26 1h27 1h28 1hck 1hcl 1jst 1jsu 1jsv 1jvp 1ke5 1ke6 1ke7 1ke8 1ke9 1ogu 1oi9 1oiq 1oir 1oit 1oiu 1oiy 1okv 1okw 1ol1 1ol2 1p2a 1p5e 1pf8 1pkd 1pw2 1pxi 1pxj 1pxk 1pxl 1pxm 1pxn 1pxo 1pxp 1pye 1qmz 1r78 1urc 1urw 1v1k 1vyw 1vyz 1w0x 1w8c 1w98 1wcc 1y8y 1y91 1ykr 2a0c 2a4l 2b52 2b53 2b54 2b55 2bhe 2bhh 2bkz 2bpm 2btr 2bts 2c4g 2c5n 2c5o 2c5v 2c5x 2c5y 2c68 2c69 2c6i 2c6k 2c6l 2c6m 2c6o 2c6t 2cch 2cci 2cjm 2clx 2ds1 2duv 2exm 2fvd 2g9x 2hic 2i40 2iw6 2iw8 2iw9 2j9m 2jgz 2r3f 2r3g 2r3h 2r3i 2r3j 2r3k 2r3l 2r3m 2r3n 2r3o 2r3p 2r3q 2r3r 2r64 2uue 2uzb 2uzd 2uze 2uzl 2uzn 2uzo 2v0d 2v22 2vta 2vth 2vti 2vtj 2vtl 2vtm 2vtn 2vto 2vtp 2vtq 2vtr 2vts 2vtt 2vu3 2vv9 2w05 2w06 2w17 2w1h 2wev 2wfy 2whb 2wih 2wip 2wma 2wmb 2wpa 2wxv 2x1n 2xmy 2xnb 3bht 3bhu 3bhv 3ddp 3ddq 3dog 3eid 3ej1 3eoc 3ezr 3ezv 3f5x 3fz1 3ig7 3igg 3le6 3lfn 3lfq 3lfs 3my5 3ns9 3pj8 3pxf 3pxq 3pxr 3pxy 3pxz 3py0 3py1 3qhr 3qhw 3ql8 3qqf 3qqg 3qqh 3qqj 3qqk 3qql 3qrt 3qru 3qtq 3qtr 3qts 3qtu 3qtw 3qtx 3qtz 3qu0 3qwj 3qwk 3qx2 3qx4 3qxo 3qxp 3qzf 3qzg 3qzh 3qzi 3r1q 3r1s 3r1y 3r28 3r6x 3r71 3r73 3r7e 3r7i 3r7u 3r7v 3r7y 3r83 3r8l 3r8m 3r8p 3r8u 3r8v 3r8z 3r9d 3r9h 3r9n 3r9o 3rah 3rai 3rak 3ral 3rjc 3rk5 3rk7 3rk9 3rkb 3rm6 3rm7 3rmf 3rni 3roy 3rpo 3rpr 3rpv 3rpy 3rzb 3s00 3s0o 3s1h 3s2p 3sqq 3sw4 3sw7 3ti1 3tiy 3tiz 3tnw 3uli 3unj 3unk 3wbl 4acm 4bck 4bcm 4bcn 4bco 4bcp 4bcq 4bgh 4bzd 4cfm 4cfn 4cfu 4cfv 4cfw 4cfx 4d1x 4d1z 4ek3 4ek4 4ek5 4ek6 4ek8 4eoi 4eoj 4eok 4eol 4eom 4eon 4eoo 4eop 4eoq 4eor 4eos 4erw 4ez3 4ez7 4fkg 4fki 4fkj 4fkl 4fko 4fkp 4fkq 4fkr 4fks 4fkt 4fku 4fkv 4fkw 4fx3 4gcj 4ii5 4kd1 4lyn 4nj3 4rj3 5a14 5and 5ane 5ang 5ani 5anj 5ank 5ano 5cyi 5d1j 5fp5 5fp6 5iev 5iex 5iey 5if1 5jq5 5jq8 5k4j 5l2w 5lmk 5lqe 5nev 5uq1 5uq2 5uq3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4I3Z)