Kinase expression constructs

Information

Background:

The aim is to select a panel of kinases suitable for E. coli expression in 96-well plates.
Ideally, the kinase catalytic domain is to be expressed in isolation.
Plasmids are provided from three libraries: Construct spans are provided from PDB entries with E. coli expression system annotations, and from the SGC Oxford plasmid library (only plasmids known to express well in E. coli).

Custom selection procedure:

Description of table fields with details of selection procedure:

targetID Kinase domain targets are given an identifier consisting of UniProt entry name followed by the kinase domain index (since some kinases have two catalytic domains)
DB_target_rank Qualitative ranking of human kinase importance, based on metrics such as number of bioassays, number of PDBs, number of publications, % mutation rate in sequenced tumor samples
plasmid_ID For a given kinase target, all matching plasmids from the available plasmid libraries (see plasmid_source) are aligned and sorted based on nconflicts and nextraneous_residues (see below), and the top-ranked plasmid is selected (click the targetID to see the alignment)
plasmid_source Source of the top-ranked plasmid. Two plasmid libraries are currently available to the Chodera lab - SGC Oxford and HIP pJP1520. Only SGC Oxford plasmids suitable for E. coli expression are included in this selection procedure.
plasmid_nconflicts Number of conflicts between plasmid and UniProt sequence in the region of the target domain
plasmid_nextraneous_residues Number of plasmid residues outside the target domain region
nPDBs Number of PDB constructs matching the target gene, from any species, and with an E. coli expression system annotation
top_pdb_ID Matching PDB constructs are ranked by auth_score (see below), nextraneous_residues, and nconflicts, and the top-ranked PDB (and chain ID) is selected
top_pdb_expr_tag Type of expression tag detected for top-ranked PDB construct
top_pdb_auth_score Authenticity score assigned to top-ranked PDB construct based on the expression tag detected. Currently this is only used to distinguish between constructs with expression tags (auth_score > 0) and those without (auth_score = 0)
top_pdb_nextraneous_residues Number of PDB construct residues outside the target domain region
family UniProt protein family annotation
top_pdb_taxname Source organism of the top-ranked PDB construct
selected_construct_source Selected constructs will ultimately be full-length SGC Oxford plasmids or PDB constructs (to be subcloned from either SGC Oxford or HIP plasmids).
selected_construct_nextraneous_residues nextraneous_residues for the selected construct

Other notes:

Sort table by clicking on column headers. Shift-click for multicolumn sorting. Drag-click to rearrange columns. Refresh page to reset.
Click on the targetID to see alignments of plasmids and PDB constructs against the target UniProt sequence (kinase catalytic domain highlighted in red).

Table of kinase expression constructs

targetID DB_target_rank plasmid_ID plasmid_source plasmid_nconflicts plasmid_nextraneous_residues nPDBs top_pdb_ID top_pdb_expr_tag top_pdb_auth_score top_pdb_nextraneous_residues family top_pdb_taxname selected_construct_source selected_construct_nextraneous_residues caliper(ng/ul) yield(ug/mL_culture)
0 MKNK2_HUMAN_D0 251 HsCD00037986 HIP pJP1520 3 113 3 2AC5_A TEV_cleaved_Nterm 2 15 CAMK Human PDB 15 -- --
1 NEK2_HUMAN_D0 89 HsCD00038233 HIP pJP1520 0 181 20 2XKE_A Histag_Cterm 2 16 NEK Human PDB 16 -- --
2 FAK1_HUMAN_D0 32 HsCD00038381 HIP pJP1520 0 747 2 2IJM_B TEV_cleaved_Nterm 2 23 TK Human PDB 23 -- --
3 MKNK1_HUMAN_D0 214 HsCD00038677 HIP pJP1520 4 140 2 2HW6_B TEV_cleaved_Nterm 2 23 CAMK Human PDB 23 -- --
4 BRAF_HUMAN_D0 4 HsCD00038362 HIP pJP1520 0 505 8 4JVG_D TEV_cleaved_Nterm 2 24 TKL Human PDB 24 -- --
5 DAPK1_HUMAN_D0 180 HsCD00038376 HIP pJP1520 1 1168 39 1IG1_A manually selected 10 32 CAMK Human PDB 32 18 2.5
6 MST4_HUMAN_D0 308 HsCD00038628 HIP pJP1520 0 165 5 4FZD_B TEV_cleaved_Nterm 2 33 STE Human PDB 33 -- --
7 E2AK2_HUMAN_D0 135 HsCD00038350 HIP pJP1520 0 279 5 3UIU_A Histag_Cterm 2 35 -- Human PDB 35 87 11.7
8 EPHB2_HUMAN_D0 91 HsCD00038588 HIP pJP1520 1 723 7 3ZFM_A TEV_cleaved_Nterm 2 35 TK Human PDB 35 188 25.1
9 EPHB3_HUMAN_D0 202 HsCD00038757 HIP pJP1520 0 735 2 3ZFY_B TEV_cleaved_Nterm 2 35 TK Human PDB 35 13 1.8
10 ABL1_HUMAN_D0 12 HsCD00038619 HIP pJP1520 0 879 31 3UE4_A TEV_cleaved_Nterm 2 36 TK Human PDB 36 19 2.5
11 M3K5_HUMAN_D0 151 HsCD00038752 HIP pJP1520 0 1116 4 2CLQ_B TEV_cleaved_Nterm 2 37 STE Human PDB 37 105 14.0
12 STK10_HUMAN_D0 126 HsCD00038077 HIP pJP1520 0 710 6 4AOT_B TEV_cleaved_Nterm 2 44 STE Human PDB 44 28 3.8
13 KS6A3_HUMAN_D0 49 HsCD00038078 HIP pJP1520 0 481 4 4GUE_A TEV_cleaved_Nterm 2 46 AGC Mouse PDB 46 -- --
14 CSK22_HUMAN_D0 154 HsCD00037966 HIP pJP1520 0 65 2 3E3B_X other_extra_seq_Nterm 1 54 -- Human PDB 54 134 17.9
15 PAK1_HUMAN_D0 157 HsCD00038597 HIP pJP1520 1 294 17 3Q52_A Histag_Cterm 2 55 STE Human PDB 55 -- --
16 MP2K4_HUMAN_D0 181 HsCD00038296 HIP pJP1520 0 133 6 3VUT_B Histag_Cterm 2 62 STE Human PDB 62 -- --
17 MARK2_HUMAN_D0 237 HsCD00038251 HIP pJP1520 0 504 20 3IEC_D other_extra_seq_Nterm 1 68 CAMK Human PDB 68 -- --
18 MK01_HUMAN_D0 16 HsCD00038281 HIP pJP1520 0 72 61 4FMQ_A TEV_cleaved_Nterm 2 74 CMGC Human PDB 74 84 11.2
19 MK08_HUMAN_D0 36 HsCD00038084 HIP pJP1520 0 89 32 1UKH_A Histag_Cterm 2 74 CMGC Human PDB 74 214 28.5
20 STRAA_HUMAN_D0 402 HsCD00037995 HIP pJP1520 0 92 1 3GNI_B TEV_uncleaved_Nterm 2 79 STE Human PDB 79 -- --
21 MELK_HUMAN_D0 137 HsCD00038574 HIP pJP1520 0 399 2 4BFM_A Histag_Cterm 2 82 CAMK Mouse PDB 82 -- --
22 CSKP_HUMAN_D0 111 HsCD00038384 HIP pJP1520 0 633 10 3TAC_A Histag_Nterm 2 97 CAMK Human PDB 97 76 10.1
23 CLK1_HUMAN_D0 171 CLK1A-c007 SGC Oxford 1 21 2 2VAG_A TEV_cleaved_Nterm 2 23 CMGC Human SGC 21 -- --
24 HASP_HUMAN_D0 371 GSG2A-c009 SGC Oxford 0 42 7 2VUW_A TEV_cleaved_Nterm 2 22 -- Human PDB 22 17 2.3
25 MP2K6_HUMAN_D0 222 MAP2K6A-c025 SGC Oxford 2 27 2 3FME_A TEV_cleaved_Nterm 2 29 STE Human SGC 27 -- --
26 CDKL1_HUMAN_D0 361 CDKL1A-c024 SGC Oxford 4 42 3 4AGU_B TEV_Cterm 2 28 CMGC Human PDB 28 174 23.2
27 BMPR2_HUMAN_D0 78 BMPR2A-c019 SGC Oxford 0 34 2 3G2F_A Histag_Cterm 2 35 TKL Human SGC 34 106 14.1
28 KC1G1_HUMAN_D0 276 CSNK1G1A-c013 SGC Oxford 1 59 1 2CMW_A TEV_cleaved_Nterm 2 39 CK1 Human PDB 39 256 34.1
29 DYR1A_HUMAN_D0 83 DYRK1AA-c004 SGC Oxford 0 61 25 4MQ2_C TEV_cleaved_Nterm 2 41 CMGC Human PDB 41 256 34.1
30 KC1G2_HUMAN_D0 238 CSNK1G2A-c002 SGC Oxford 1 41 4 2C47_A TEV_cleaved_Nterm 2 43 CK1 Human SGC 41 57 7.6
31 STK16_HUMAN_D0 302 STK16A-c002 SGC Oxford 1 43 2 2BUJ_B TEV_uncleaved_Nterm 2 44 -- Human SGC 43 155 20.6
32 TTK_HUMAN_D0 158 TTKA-c013 SGC Oxford 0 46 20 3H9F_A TEV_uncleaved_Nterm 2 47 -- Human SGC 46 -- --
33 KCC2A_HUMAN_D0 376 CAMK2AA-c026 SGC Oxford 0 54 3 2VZ6_B TEV_uncleaved_Nterm 2 55 CAMK Human SGC 54 2 0.2
34 VRK2_HUMAN_D0 354 VRK2A-c017 SGC Oxford 0 54 2 2V62_B TEV_uncleaved_Nterm 2 55 CK1 Human SGC 54 9 1.2
35 VRK3_HUMAN_D0 445 VRK3A-c016 SGC Oxford 0 60 2 2JII_A TEV_uncleaved_Nterm 2 61 CK1 Human SGC 60 506 67.4
36 PMYT1_HUMAN_D0 304 PKMYT1A-c004 SGC Oxford 0 61 1 3P1A_A TEV_uncleaved_Nterm 2 62 -- Human SGC 61 285 38.1
37 CLK3_HUMAN_D0 223 CLK3A-c005 SGC Oxford 0 64 6 2WU7_A TEV_uncleaved_Nterm 2 65 CMGC Human SGC 64 -- --
38 GAK_HUMAN_D0 201 GAKA-c006 SGC Oxford 0 84 6 4O38_A TEV_cleaved_Nterm 2 64 -- Human PDB 64 485 64.7
39 PAK7_HUMAN_D0 236 PAK5A-c011 SGC Oxford 0 66 2 2F57_B TEV_uncleaved_Nterm 2 66 STE Human SGC 66 110 14.7
40 SLK_HUMAN_D0 207 SLKA-c004 SGC Oxford 0 66 4 2JFL_A TEV_uncleaved_Nterm 2 67 STE Human SGC 66 12 1.7
41 ST17B_HUMAN_D0 279 STK17BA-c014 SGC Oxford 0 66 2 3LM0_A TEV_uncleaved_Nterm 2 67 CAMK Human SGC 66 -- --
42 KCC4_HUMAN_D0 224 CAMK4A-c007 SGC Oxford 0 72 1 2W4O_A TEV_uncleaved_Nterm 2 95 CAMK Human SGC 72 3 0.4
43 KCC2G_HUMAN_D0 218 CAMK2GA-c006 SGC Oxford 1 77 1 2V7O_A TEV_uncleaved_Nterm 2 78 CAMK Human SGC 77 100 13.4
44 KC1G3_HUMAN_D0 294 CSNK1G3A-c002 SGC Oxford 1 80 9 2CHL_A TEV_uncleaved_Nterm 2 81 CK1 Human SGC 80 422 56.3
45 MK11_HUMAN_D0 159 MAPK11A-c007 SGC Oxford 0 84 5 3GP0_A TEV_cleaved_Nterm 2 64 CMGC Human SGC 84 238 31.7
46 KS6A1_HUMAN_D1 132 RPS6KA1A-c036 SGC Oxford 0 88 2 3RNY_B Histag_Nterm 2 89 AGC Human SGC 88 43 5.7
47 NEK1_HUMAN_D0 141 NEK1A-c011 SGC Oxford 1 95 4 4APC_A TEV_uncleaved_Nterm 2 96 NEK Human SGC 95 25 3.4
48 PHKG2_HUMAN_D0 134 PHKG2A-c020 SGC Oxford 0 97 4 2Y7J_D TEV_uncleaved_Nterm 2 98 CAMK Human SGC 97 10 1.3
49 DYRK2_HUMAN_D0 250 DYRK2A-c023 SGC Oxford 0 103 3 4AZF_A TEV_uncleaved_Nterm 2 104 CMGC Human SGC 103 18 2.4
50 DMPK_HUMAN_D0 110 DMPK1A-c026 SGC Oxford 0 164 2 2VD5_B TEV_cleaved_Nterm 2 144 AGC Human PDB 144 57 7.6
51 MRCKA_HUMAN_D0 232 CDC42BPAA-c004 SGC Oxford 4 171 1 4AW2_A TEV_Cterm 2 171 AGC Rat SGC 171 -- --
52 CSK_HUMAN_D0 148 23941 addgene 0 195 4 3D7T_A other_extra_seq_Nterm 1 15 TK Human PDB 15 469 62.6
53 CDK2_HUMAN_D0 26 23777 addgene 0 15 229 4EOO_A TEV_cleaved_Nterm 2 17 CMGC Human PDB 17 23 3.0
54 CDK6_HUMAN_D0 314 23688 addgene 0 38 2 4EZ5_A Histag_Cterm 2 20 CMGC Human PDB 20 -- --
55 DAPK3_HUMAN_D0 198 23436 addgene 0 192 6 3BHY_A TEV_cleaved_Nterm 2 21 CAMK Human PDB 21 30 3.9
56 EPHB4_HUMAN_D0 96 23896 addgene 0 702 2 3ZEW_A TEV_cleaved_Nterm 2 21 TK Human PDB 21 -- --
57 AURKA_HUMAN_D0 43 23532 addgene 0 153 87 2NP8_A TEV_cleaved_Nterm 2 22 -- Human PDB 22 8 1.1
58 FAK2_HUMAN_D0 76 23898 addgene 0 750 2 3CC6_A TEV_cleaved_Nterm 2 23 TK Human PDB 23 2 0.2
59 AAPK2_HUMAN_D0 194 23671 addgene 0 299 5 2H6D_A TEV_cleaved_Nterm 2 24 CAMK Human PDB 24 8 1.1
60 FGFR2_HUMAN_D0 17 23904 addgene 0 550 40 3RI1_B TEV_cleaved_Nterm 2 26 TK Human PDB 26 -- --
61 KC1D_HUMAN_D0 93 23796 addgene 0 146 10 4HNF_B TEV_cleaved_Nterm 2 28 CK1 Human PDB 28 28 3.7
62 KC1E_HUMAN_D0 233 23797 addgene 0 147 14 4HNI_A TEV_cleaved_Nterm 2 28 CK1 Human PDB 28 26 3.5
63 VGFR1_HUMAN_D0 19 23912 addgene 0 1006 1 3HNG_A TEV_cleaved_Nterm 2 29 TK Human PDB 29 4 0.5
64 FGFR1_HUMAN_D0 11 23922 addgene 0 530 28 3KY2_A Histag_Nterm 2 30 TK Human PDB 30 46 6.2
65 SRC_HUMAN_D0 10 23934 addgene 0 282 97 4MXO_A TEV_cleaved_Nterm 2 33 TK Human PDB 33 165 22.1
66 EPHB1_HUMAN_D0 182 23930 addgene 0 720 9 3ZFX_F TEV_cleaved_Nterm 2 35 TK Human PDB 35 217 28.9
67 KCC2B_HUMAN_D0 249 23820 addgene 0 244 4 3BHH_D TEV_cleaved_Nterm 2 37 CAMK Human PDB 37 53 7.1
68 FGFR3_HUMAN_D0 13 23933 addgene 0 516 1 4K33_A Histag_Nterm 2 38 TK Human PDB 38 17 2.3
69 PIM1_HUMAN_D0 77 23692 addgene 0 60 91 2O65_A Histag_Cterm 2 41 CAMK Human PDB 41 -- --
70 AURKB_HUMAN_D0 40 23682 addgene 0 93 1 4AF3_A TEV_cleaved_Nterm 2 42 -- Human PDB 42 -- --
71 MERTK_HUMAN_D0 98 23900 addgene 0 727 12 3BPR_B Histag_Nterm 2 42 TK Human PDB 42 126 16.7
72 CDK16_HUMAN_D0 257 23754 addgene 0 214 1 3MTL_A Histag_Cterm 2 43 CMGC Human PDB 43 202 26.9
73 KCC2D_HUMAN_D0 172 23814 addgene 0 219 3 2VN9_A TEV_cleaved_Nterm 2 43 CAMK Human PDB 43 12 1.6
74 STK24_HUMAN_D0 274 23595 addgene 0 180 11 3ZHP_C TEV_uncleaved_Nterm 2 44 STE Human PDB 44 6 0.8
75 NEK7_HUMAN_D0 299 23395 addgene 0 37 2 2WQN_A Histag_Cterm 2 45 NEK Human PDB 45 10 1.3
76 STK3_HUMAN_D0 219 23818 addgene 0 239 10 4LG4_B TEV_cleaved_Nterm 2 48 STE Human PDB 48 257 34.3
77 KCC1G_HUMAN_D0 305 23813 addgene 0 221 2 2JAM_A TEV_cleaved_Nterm 2 50 CAMK Human PDB 50 2 0.3
78 MET_HUMAN_D0 6 23889 addgene 0 1140 6 4EEV_A Histag_Nterm 2 50 TK Human PDB 50 -- --
79 PAK4_HUMAN_D0 162 23713 addgene 0 339 24 2J0I_A TEV_cleaved_Nterm 2 52 STE Human PDB 52 179 23.9
80 CSK21_HUMAN_D0 62 23678 addgene 0 105 79 3AXW_A other_extra_seq_Nterm 1 55 -- Human PDB 55 109 14.6
81 PLK2_HUMAN_D0 190 23691 addgene 0 432 5 4I5P_A Histag_Nterm 2 56 -- Human PDB 56 -- --
82 MP2K2_HUMAN_D0 88 23555 addgene 0 102 2 1S9I_A Histag_Cterm 2 57 STE Human PDB 57 -- --
83 CHK2_HUMAN_D0 24 23843 addgene 0 276 44 2CN5_A other_extra_seq_Nterm 1 63 CAMK Human PDB 63 61 8.2
84 MAPK2_HUMAN_D0 75 23426 addgene 1 122 77 2JBO_A TEV_cleaved_Nterm 2 65 CAMK Human PDB 65 -- --
85 PAK6_HUMAN_D0 282 23833 addgene 0 429 3 2C30_A TEV_uncleaved_Nterm 2 70 STE Human PDB 70 135 18.0
86 MAPK3_HUMAN_D0 372 23790 addgene 0 121 4 3FXW_A TEV_uncleaved_Nterm 2 76 CAMK Human PDB 76 141 18.8
87 MARK3_HUMAN_D0 366 23716 addgene 0 477 4 2QNJ_A other_extra_seq_Nterm 1 77 CAMK Human PDB 77 8 1.0
88 MK14_HUMAN_D0 14 23865 addgene 0 75 234 2Y8O_A TEV_cleaved_Nterm 2 78 CMGC Human PDB 78 530 70.7
89 VRK1_HUMAN_D0 384 23496 addgene 0 116 4 3OP5_D TEV_cleaved_Nterm 2 84 CK1 Human PDB 84 467 62.3
90 MK13_HUMAN_D0 240 23739 addgene 0 81 4 4EYJ_A Histag_Nterm 2 88 CMGC Human PDB 88 238 31.7
91 MK03_HUMAN_D0 52 23509 addgene 0 91 2 2ZOQ_B other_extra_seq_Nterm 1 94 CMGC Human PDB 94 273 36.3
92 EPHA3_HUMAN_D0 95 23911 addgene 0 721 21 4GK2_A Histag_Nterm 2 100 TK Human PDB 100 106 14.2
93 KAPCA_HUMAN_D0 63 23495 addgene 0 97 162 4IAC_A Histag_Nterm 2 102 AGC Mouse PDB 102 7 1.0
94 FES_HUMAN_D0 119 23876 addgene 0 560 4 3CBL_A TEV_cleaved_Nterm 2 116 TK Human PDB 116 330 43.9
95 AAPK1_HUMAN_D0 183 23871 addgene 0 297 1 4CFH_A TEV_uncleaved_Nterm 2 241 CAMK Rat PDB 241 -- --