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(-) Description

Title :  STRUCTURE OF PHOPSHO-CDK2-CYCLIN A IN COMPLEX WITH AN ATP-COMPETITIVE INHIBITOR
 
Authors :  A. Echalier
Date :  01 Aug 16  (Deposition) - 25 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Cdk2; Cyclin A, Cell Cycle, Transferase, Inhibitor, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hylsova, B. Carbain, J. Fanfrlik, L. Musilova, S. Haldar, C. Kopruluoglu, H. Ajani, P. S. Brahmkshatriya, R. Jorda, V. Krystof, P. Hobza, A. Echalier, K. Paruch, M. Lepsik
Explicit Treatment Of Active-Site Waters Enhances Quantum Mechanical/Implicit Solvent Scoring: Inhibition Of Cdk2 By New Pyrazolo[1, 5-A]Pyrimidines.
Eur J Med Chem V. 126 1118 2016
PubMed-ID: 28039837  |  Reference-DOI: 10.1016/J.EJMECH.2016.12.023

(-) Compounds

Molecule 1 - CYCLIN-DEPENDENT KINASE 2
    Chains: A
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    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 Taxid: 562
    Gene: CCNA2, CCN1, CCNA
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYCLIN-A
 
Molecule 3 - CYCLIN-DEPENDENT KINASE 2
    Chains: C
    EC Number: 2.7.11.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CDK2, CDKN2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CELL DIVISION PROTEIN KINASE 2,P33 PROTEIN KINASE

 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  (4, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
16ZK2Ligand/Ion4-[4-[3-BROMANYL-7-(PYRIDIN-3-YLMETHYLAMINO)PYRAZOLO[1,5-A]PYRIMIDIN-5-YL]PHENYL]BENZAMIDE
2MG1Ligand/IonMAGNESIUM ION
3SGM2Ligand/IonMONOTHIOGLYCEROL
4TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
16ZK1Ligand/Ion4-[4-[3-BROMANYL-7-(PYRIDIN-3-YLMETHYLAMINO)PYRAZOLO[1,5-A]PYRIMIDIN-5-YL]PHENYL]BENZAMIDE
2MG-1Ligand/IonMAGNESIUM ION
3SGM1Ligand/IonMONOTHIOGLYCEROL
4TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
16ZK1Ligand/Ion4-[4-[3-BROMANYL-7-(PYRIDIN-3-YLMETHYLAMINO)PYRAZOLO[1,5-A]PYRIMIDIN-5-YL]PHENYL]BENZAMIDE
2MG-1Ligand/IonMAGNESIUM ION
3SGM1Ligand/IonMONOTHIOGLYCEROL
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:10 , GLU A:12 , ALA A:31 , PHE A:80 , GLU A:81 , PHE A:82 , LEU A:83 , HIS A:84 , LYS A:129 , GLN A:131 , LEU A:134 , HOH A:453binding site for residue 6ZK A 301
2AC2SOFTWAREMET B:189 , LYS B:192 , CYS B:193 , ARG B:241 , ASP B:305binding site for residue SGM B 501
3AC3SOFTWAREMET B:200 , GLN B:203 , ILE B:206binding site for residue MG B 502
4AC4SOFTWAREILE C:10 , GLU C:12 , ALA C:31 , PHE C:80 , GLU C:81 , PHE C:82 , LEU C:83 , HIS C:84 , GLN C:85 , ASP C:86 , LYS C:89 , GLN C:131 , LEU C:134 , HOH C:425binding site for residue 6ZK C 301
5AC5SOFTWARELYS D:192 , CYS D:193 , ARG D:241 , ASP D:305binding site for residue SGM D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5LMK)

(-) Cis Peptide Bonds  (5, 5)

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
5Asp D:345 -Pro D:346

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5LMK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5LMK)

(-) Exons   (0, 0)

(no "Exon" information available for 5LMK)

(-) 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:297
                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....eeeeeee.....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
                 5lmk A   0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYtHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL 298
                                     9        19        29        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       291       
                                                                 38|                                                                                                                    160-TPO                                                                                                                                      
                                                                  41                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lmk B 175 VPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL 432
                                   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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee.....eeeeeee.....eeeeeeee........hhhhhhhhhhhhhh.......eeeeee...eeeeeee...eehhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh....hhhhhhhhhhhh........hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lmk C   0 SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYtHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHL 296
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159|      169       179       189       199       209       219||     260       270       280       290      
                                                                                                                                                                                          160-TPO                                                     220|                                            
                                                                                                                                                                                                                                                       252                                            


Chain D from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh....hhhhhhhh.....hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lmk D 176 PDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL 432
                                   185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425
   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 5LMK)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5LMK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5LMK)

(-) Gene Ontology  (84, 95)

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  5lmk
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  2.7.11.22
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 Related Entries

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

UniProtKB/Swiss-Prot
        CCNA2_HUMAN | P20248: 1e9h 1fin 1fvv 1gy3 1h1p 1h1q 1h1r 1h1s 1h24 1h25 1h26 1h27 1h28 1jst 1jsu 1ogu 1oi9 1oiu 1oiy 1okv 1okw 1ol1 1ol2 1p5e 1pkd 1qmz 1urc 1vyw 2bkz 2bpm 2c4g 2c5n 2c5o 2c5v 2c5x 2c6t 2cch 2cci 2cjm 2i40 2iw6 2iw8 2iw9 2uue 2uzb 2uzd 2uze 2uzl 2v22 2wev 2wfy 2whb 2wih 2wip 2wma 2wmb 2wpa 2wxv 2x1n 3eid 3ej1 3eoc 3f5x 4bck 4bcm 4bcn 4bcp 4cfm 4cfn 4cfu 4cfv 4cfw 4cfx 4eoi 4eoj 4eok 4eol 4eom 4eon 4eoo 4eop 4eoq 4eor 4eos 4fx3 5cyi 5if1 5lqe 5nev
        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 4i3z 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 5lqe 5nev 5uq1 5uq2 5uq3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5LMK)