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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KINASE DOMAIN OF BRUTON'S TYROSINE KINASE WITH MUTATIONS IN THE ACTIVATION LOOP
 
Authors :  Q. Wang, C. E. Rosen, J. Kuriyan
Date :  16 Feb 15  (Deposition) - 18 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Btk, Kinase Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Wang, E. M. Vogan, L. M. Nocka, C. E. Rosen, J. A. Zorn, S. C. Harrison, J. Kuriyan
Autoinhibition Of Bruton'S Tyrosine Kinase (Btk) And Activation By Soluble Inositol Hexakisphosphate.
Elife V. 4 2015
PubMed-ID: 25699547  |  Reference-DOI: 10.7554/ELIFE.06074

(-) Compounds

Molecule 1 - NON-SPECIFIC PROTEIN-TYROSINE KINASE
    Chains: A, B, C, D
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: KINASE DOMAIN (UNP 395-659)
    Gene: BTK
    Mutation: YES
    Organism Common: BOVINE
    Organism Scientific: BOS TAURUS
    Organism Taxid: 9913

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
17464Ligand/Ion4-TERT-BUTYL-N-[2-METHYL-3-(4-METHYL-6-{[4-(MORPHOLIN-4-YLCARBONYL)PHENYL]AMINO}-5-OXO-4,5-DIHYDROPYRAZIN-2-YL)PHENYL]BENZAMIDE
2BME3Ligand/IonBETA-MERCAPTOETHANOL
3GOL8Ligand/IonGLYCEROL
4PE42Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
17461Ligand/Ion4-TERT-BUTYL-N-[2-METHYL-3-(4-METHYL-6-{[4-(MORPHOLIN-4-YLCARBONYL)PHENYL]AMINO}-5-OXO-4,5-DIHYDROPYRAZIN-2-YL)PHENYL]BENZAMIDE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3GOL1Ligand/IonGLYCEROL
4PE4-1Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Biological Unit 2 (4, 5)
No.NameCountTypeFull Name
17461Ligand/Ion4-TERT-BUTYL-N-[2-METHYL-3-(4-METHYL-6-{[4-(MORPHOLIN-4-YLCARBONYL)PHENYL]AMINO}-5-OXO-4,5-DIHYDROPYRAZIN-2-YL)PHENYL]BENZAMIDE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3GOL2Ligand/IonGLYCEROL
4PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Biological Unit 3 (4, 4)
No.NameCountTypeFull Name
17461Ligand/Ion4-TERT-BUTYL-N-[2-METHYL-3-(4-METHYL-6-{[4-(MORPHOLIN-4-YLCARBONYL)PHENYL]AMINO}-5-OXO-4,5-DIHYDROPYRAZIN-2-YL)PHENYL]BENZAMIDE
2BME1Ligand/IonBETA-MERCAPTOETHANOL
3GOL1Ligand/IonGLYCEROL
4PE41Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Biological Unit 4 (2, 5)
No.NameCountTypeFull Name
17461Ligand/Ion4-TERT-BUTYL-N-[2-METHYL-3-(4-METHYL-6-{[4-(MORPHOLIN-4-YLCARBONYL)PHENYL]AMINO}-5-OXO-4,5-DIHYDROPYRAZIN-2-YL)PHENYL]BENZAMIDE
2BME-1Ligand/IonBETA-MERCAPTOETHANOL
3GOL4Ligand/IonGLYCEROL
4PE4-1Ligand/Ion2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:408 , PHE A:413 , VAL A:416 , ALA A:428 , LYS A:430 , THR A:474 , GLU A:475 , TYR A:476 , MET A:477 , ALA A:478 , ASN A:479 , GLY A:480 , ASN A:526 , LEU A:528 , ASP A:539 , TYR A:551 , HOH A:862 , HOH A:903 , HOH A:961binding site for residue 746 A 701
02AC2SOFTWAREGLU A:455 , ASN A:530 , GLN A:532 , LYS A:536 , HOH A:933 , HOH A:966 , GLN B:467 , PRO B:469binding site for residue GOL A 702
03AC3SOFTWARELYS A:430 , VAL A:458 , LEU A:460 , THR A:474 , SER A:538 , ASP A:539 , PHE A:540 , HOH A:968binding site for residue BME A 703
04AC4SOFTWARELEU B:408 , GLY B:411 , PHE B:413 , VAL B:416 , ALA B:428 , LYS B:430 , THR B:474 , GLU B:475 , TYR B:476 , MET B:477 , ALA B:478 , GLY B:480 , ASN B:526 , LEU B:528 , ASP B:539 , VAL B:546 , HOH B:864 , HOH B:917 , HOH B:964binding site for residue 746 B 701
05AC5SOFTWARESER A:438 , GLU A:441 , HIS B:609 , HOH B:817 , HOH B:927 , HOH B:1017binding site for residue GOL B 702
06AC6SOFTWAREGLN B:516 , PHE B:517 , LEU B:518 , GLY B:541 , HOH B:833binding site for residue GOL B 703
07AC7SOFTWARELYS B:430 , MET B:449 , VAL B:458 , LEU B:460 , ASP B:539 , PHE B:540 , HOH B:877 , HOH B:982binding site for residue BME B 704
08AC8SOFTWARETYR A:485 , MET A:489 , GLN A:497 , ASP A:531 , GLN B:412 , VAL B:415 , LYS B:433 , HOH B:1026binding site for residue PE4 B 705
09AC9SOFTWARELEU C:408 , GLY C:411 , PHE C:413 , VAL C:416 , ALA C:428 , LYS C:430 , THR C:474 , GLU C:475 , TYR C:476 , MET C:477 , ALA C:478 , GLY C:480 , ASN C:526 , LEU C:528 , ASP C:539 , VAL C:546 , HOH C:1174 , HOH C:1222 , HOH C:1269binding site for residue 746 C 1001
10AD1SOFTWAREGLN C:516 , PHE C:517 , LEU C:518 , GLY C:541 , HOH C:1129 , HOH C:1288binding site for residue GOL C 1002
11AD2SOFTWARELYS C:430 , MET C:449 , VAL C:458 , ASP C:539 , PHE C:540 , HOH C:1189 , HOH C:1290binding site for residue BME C 1003
12AD3SOFTWAREGLY C:411 , GLN C:412 , LYS C:433 , HOH C:1102 , HOH C:1130 , TYR D:485 , MET D:489 , GLN D:497 , ASP D:531binding site for residue PE4 C 1004
13AD4SOFTWARELEU D:408 , PHE D:413 , VAL D:416 , ALA D:428 , LYS D:430 , THR D:474 , GLU D:475 , TYR D:476 , MET D:477 , ALA D:478 , ASN D:479 , GLY D:480 , ASN D:526 , LEU D:528 , ASP D:539 , VAL D:546 , TYR D:551 , HOH D:886 , HOH D:924 , HOH D:993binding site for residue 746 D 701
14AD5SOFTWARELYS D:430 , MET D:449 , VAL D:458 , LEU D:460 , ASP D:539 , PHE D:540 , HOH D:906 , HOH D:939 , HOH D:982binding site for residue GOL D 702
15AD6SOFTWAREGLN C:467 , PRO C:469 , ASN D:530 , GLN D:532 , VAL D:534 , LYS D:536 , HOH D:853 , HOH D:976binding site for residue GOL D 703
16AD7SOFTWAREPHE D:517 , LEU D:518 , GLY D:541 , HOH D:1033binding site for residue GOL D 704
17AD8SOFTWARESER B:572 , PHE B:574 , ALA D:611 , GLN D:612 , GLU D:636 , HOH D:854binding site for residue GOL D 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y95)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Arg A:468 -Pro A:469
2Arg B:468 -Pro B:469
3Arg C:468 -Pro C:469
4Arg D:468 -Pro D:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y95)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y95)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y95)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeeee..eeeeeeee...eeeeeee......hhhhhhhhhhhhh.........eeeee......eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhh.hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y95 A 394 AWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGMTRFVLDDEYTSSTGTKFPVKWASPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYAIMYSCWHEKADERPTFKILLSNILDVMDEES 659
                                   403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653      


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeeee..eeeeeeee...eeeeeeee.....hhhhhhhhhhhhh.........eeeee......eeee......hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhh.hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y95 B 394 AWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGMTRFVLDDEYTSSTGTKFPVKWASPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYAIMYSCWHEKADERPTFKILLSNILDVMDEES 659
                                   403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653      


Chain C from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeeee..eeeeeeee...eeeeeee......hhhhhhhhhhhhh.........eeeee......eeee......hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhh.hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh.........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y95 C 394 AWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGMTRFVLDDEYTSSTGTKFPVKWASPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYAIMYSCWHEKADERPTFKILLSNILDVMDEES 659
                                   403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653      


Chain D from PDB  Type:PROTEIN  Length:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee...eeeeeee......hhhhhhhhhhhhh.........eeeee......eeee.....eehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...hhhhhh.hhhhhh......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y95 D 395 WEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGMTRFVLDDEYTSSTGTKFPVKWASPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLPRPHLASERVYAIMYSCWHEKADERPTFKILLSNILDVMDEES 659
                                   404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654
   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  (0, 0)

(no "SCOP Domain" information available for 4Y95)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y95)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y95)

(-) Gene Ontology  (31, 31)

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 Related Entries

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

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        Q3ZC95_BOVIN | Q3ZC95: 4y93 4y94

(-) Related Entries Specified in the PDB File

4y93 4y94