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(-) Description

Title :  CRYSTAL STRUCTURE OF P21-ACTIVATED KINASE 1 IN COMPLEX WITH AN INHIBITOR COMPOUND 29
 
Authors :  L. Rouge, W. Wang
Date :  21 May 15  (Deposition) - 01 Jul 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pak1, Kinase, Inhibitor, Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Crawford, W. Lee, I. Aliagas, S. Mathieu, K. P. Hoeflich, W. Zhou, W. Wang, L. Rouge, L. Murray, H. La, N. Liu, P. W. Fan, J. Cheong, C. E. Heise, S. Ramaswamy, R. Mintzer, Y. Liu, Q. Chao, J. Rudolph
Structure-Guided Design Of Group I Selective P21-Activated Kinase Inhibitors.
J. Med. Chem. V. 58 5121 2015
PubMed-ID: 26030457  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00572

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PAK 1
    Chains: A, B
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PROTEIN KINASE DOMAIN RESIDUE 249-545
    Gene: PAK1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ALPHA-PAK,P21-ACTIVATED KINASE 1,PAK-1,P65-PAK

 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, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
14T62Ligand/IonN~2~-[(7-CHLORO-1H-BENZIMIDAZOL-6-YL)METHYL]-N~4~-(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)PYRIMIDINE-2,4-DIAMINE
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14T61Ligand/IonN~2~-[(7-CHLORO-1H-BENZIMIDAZOL-6-YL)METHYL]-N~4~-(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)PYRIMIDINE-2,4-DIAMINE
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
14T61Ligand/IonN~2~-[(7-CHLORO-1H-BENZIMIDAZOL-6-YL)METHYL]-N~4~-(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)PYRIMIDINE-2,4-DIAMINE
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:284 , ALA A:297 , LYS A:299 , GLU A:345 , TYR A:346 , LEU A:347 , ASP A:393 , ASN A:394 , LEU A:396 , THR A:406binding site for residue 4T6 A 601
2AC2SOFTWAREARG A:388 , ARG A:421 , THR A:423binding site for residue SO4 A 602
3AC3SOFTWAREILE B:276 , ALA B:297 , GLU B:345 , TYR B:346 , LEU B:347 , ASP B:393 , ASN B:394 , LEU B:396 , THR B:406binding site for residue 4T6 B 601

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:360 -B:360

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Ser A:262 -Val A:263
2Ser A:281 -Gly A:282
3Gly A:282 -Thr A:283
4Gln B:306 -Pro B:307
5Phe B:408 -Gly B:409
6Gly B:409 -Phe B:410

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZY6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZY6)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZY6)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh....hhhhheeeeee........eeeeee.....eeeee...hhhhhhhhhhhhhh.......eeeee....eeeee....eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh.......hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zy6 A 251 EEILEKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQPKKELIINEILVMRENKNPNIVNYLDSYLVELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFCAQITPEQSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   260       270       280       290       300|      316       326       336|      348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       518       528       538    
                                                                           300|                          336|                                                                                                                                                                                                           
                                                                            307                           339                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:280
                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...hhhhheeeeeeee.....eeeeeee.....eeeeeeee.hhh.hhhhhhhhhhhhhhh.......eeeeeee..eeeeeee.....hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..................hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zy6 B 255 EKLRSIVSVGDPKKKYTRFEKIGQGASGTVYTAMDVATGQEVAIKQMNLQQQPKKELIINEILVMRENKNPNIVNYLDSYLVGDELWVVMEYLAGGSLTDVVTETCMDEGQIAAVCRECLQALEFLHSNQVIHRNIKSDNILLGMDGSVKLTDFGFSKRSTMVGTPYWMAPEVVTRKAYGPKVDIWSLGIMAIEMIEGEPPYLNENPLRALYLIATNGTPELQNPEKLSAIFRDFLNRCLEMDVEKRGSAKELLQHQFLKIAKPLSSLTPLIAAAKEATK 542
                                   264       274       284       294       304       314       324       334       344       354       364       374       384       394       404     ||422       432       442       452       462       472       482       492       502       512       522       532       542
                                                                                                                                                                                     410|                                                                                                                           
                                                                                                                                                                                      419
   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 4ZY6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZY6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZY6)

(-) Gene Ontology  (61, 61)

Asymmetric Unit(hide GO term definitions)

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  4zy6
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  PAK1_HUMAN | Q13153
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        PAK1_HUMAN | Q13153: 1f3m 1yhv 1yhw 1zsg 2hy8 2qme 3dvp 3fxz 3fy0 3q4z 3q52 3q53 4daw 4eqc 4o0r 4o0t 4p90 4zji 4zjj 4zlo 4zy4 4zy5 5dew 5dey 5dfp 5ime 5kbq 5kbr

(-) Related Entries Specified in the PDB File

4zy4 4zy5