- PDB-6i99: Bone Marrow Tyrosine Kinase in Chromosome X in complex with a new... -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 6i99
Title
Bone Marrow Tyrosine Kinase in Chromosome X in complex with a newly designed covalent inhibitor JS24
Components
Cytoplasmic tyrosine-protein kinase BMX
Keywords
CYTOSOLIC PROTEIN / Cytoplasmic tyrosine-kinase BMX / Homo Sapiens
Function / homology
Function and homology information
phosphatidylinositol biosynthetic process / Apoptotic cleavage of cellular proteins / mesoderm development / Synthesis of PIPs at the plasma membrane / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / ruffle membrane / protein tyrosine kinase activity / adaptive immune response ...phosphatidylinositol biosynthetic process / Apoptotic cleavage of cellular proteins / mesoderm development / Synthesis of PIPs at the plasma membrane / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / ruffle membrane / protein tyrosine kinase activity / adaptive immune response / protein autophosphorylation / cell adhesion / intracellular signal transduction / protein phosphorylation / apoptotic process / signal transduction / nucleoplasm / ATP binding / metal ion binding / plasma membrane / cytosol Similarity search - Function
Cytoplasmictyrosine-proteinkinaseBMX / Bone marrow tyrosine kinase gene in chromosome X protein / Epithelial and endothelial tyrosine ...Bone marrow tyrosine kinase gene in chromosome X protein / Epithelial and endothelial tyrosine kinase / ETK / NTK38
Mass: 32564.414 Da / Num. of mol.: 2 / Mutation: Q432K, Q620E, Q611M, D617T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell: Hematopoietic, endothelial, metastatic carcinoma / Gene: BMX / Variant: 2 / Plasmid: pFastBac1 / Production host: Baculovirus expression vector pFastBac1-HM References: UniProt: P51813, non-specific protein-tyrosine kinase
Resolution: 2.001→72.559 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / Phase error: 31.26 Details: NCS used between chain A and chain B TLS refinement of anisotropic ADPs - 4 non-equivalent rigid bodies were defined per protein chain. Hydrogen atoms were included in calculated positions.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.2586
1184
5.04 %
Random 5% selection
Rwork
0.2321
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-
-
obs
0.2335
23504
57.3 %
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Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: -2.2119 Å2 / ksol: 0.9549 e/Å3
Displacement parameters
Biso mean: 23.6 Å2
Refinement step
Cycle: LAST / Resolution: 2.001→72.559 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
4308
0
76
126
4510
Refine LS restraints
Refine-ID
Type
Dev ideal
Number
X-RAY DIFFRACTION
f_bond_d
0.002
4506
X-RAY DIFFRACTION
f_angle_d
0.603
6090
X-RAY DIFFRACTION
f_dihedral_angle_d
11.28
2643
X-RAY DIFFRACTION
f_chiral_restr
0.041
631
X-RAY DIFFRACTION
f_plane_restr
0.003
756
LS refinement shell
Resolution (Å)
Rfactor Rfree
Num. reflection Rfree
Rfactor Rwork
Num. reflection Rwork
Refine-ID
% reflection obs (%)
2.001-2.0917
0.446
13
0.3296
198
X-RAY DIFFRACTION
4
2.0917-2.202
0.2674
26
0.3012
558
X-RAY DIFFRACTION
11
2.202-2.3399
0.3991
78
0.3053
1342
X-RAY DIFFRACTION
28
2.3399-2.5206
0.2944
139
0.296
2384
X-RAY DIFFRACTION
50
2.5206-2.7743
0.318
177
0.284
3708
X-RAY DIFFRACTION
76
2.7743-3.1757
0.2776
225
0.2609
4771
X-RAY DIFFRACTION
98
3.1757-4.001
0.2596
242
0.2134
4702
X-RAY DIFFRACTION
96
4.001-72.559
0.2118
284
0.1926
4657
X-RAY DIFFRACTION
94
Refinement TLS params.
Method: refined / Refine-ID: X-RAY DIFFRACTION
ID
L11 (°2)
L12 (°2)
L13 (°2)
L22 (°2)
L23 (°2)
L33 (°2)
S11 (Å °)
S12 (Å °)
S13 (Å °)
S21 (Å °)
S22 (Å °)
S23 (Å °)
S31 (Å °)
S32 (Å °)
S33 (Å °)
T11 (Å2)
T12 (Å2)
T13 (Å2)
T22 (Å2)
T23 (Å2)
T33 (Å2)
Origin x (Å)
Origin y (Å)
Origin z (Å)
1
1.7889
-0.4213
0.5483
1.2474
-0.3363
1.2201
-0.128
0.2951
-0.0835
-0.1255
0.0498
-0.0015
0.0447
-0.011
-0.0062
0.2
-0.015
-0.0358
0.3334
-0.0234
0.1342
10.2146
-18.3299
10.0771
2
1.5711
-0.3009
0.6909
0.7064
0.0278
1.7043
-0.0996
0.043
-0.0564
0.027
-0.0172
-0.0375
-0.048
0.121
-0.0017
0.1168
-0.0127
-0.0239
0.1827
0.0018
0.0944
9.5551
-10.3682
22.6104
3
1.3236
-0.1999
0.6206
0.5335
0.0624
1.0167
0.0607
-0.1406
-0.0208
0.0659
-0.0447
-0.0505
0.1659
-0.1949
-0.0699
0.103
0.0035
-0.0779
0.2896
0.0511
0.0547
-0.9926
-12.7351
35.0708
4
0.2362
-0.1034
0.0509
0.396
-0.141
0.7602
0.015
-0.1819
0.0855
0.2138
-0.0775
0
0.0988
-0.0451
-0.2601
0.1388
-0.0022
-0.0506
0.1909
-0.1075
0.0535
6.222
-3.4664
42.5483
5
1.5691
0.25
-0.1372
0.239
-0.0432
0.3256
-0.0791
-0.1462
0.059
0.1403
0.0255
-0.0344
-0.0024
-0.1101
-0.0247
0.0858
0.0416
-0.0637
0.2663
-0.0269
0.0547
-25.04
-19.3519
20.7943
6
1.8712
0.6949
-0.1363
1.1325
-0.5635
1.6684
0.0214
-0.0798
-0.1749
0.1872
-0.0414
0.0991
0.0419
-0.0482
-0.0374
0.1842
-0.0059
0.0032
0.1654
-0.0253
0.1145
-29.7101
-11.6143
8.4207
7
0.2689
0.0097
-0.0333
0.2435
0.0292
0.8993
0.0664
-0.0981
0.0226
0.0502
-0.0452
-0.0139
-0.1912
-0.0046
-0.0005
0.1287
-0.0352
-0.0039
0.2216
0.0144
0.0509
-19.2233
-12.1259
5.0188
8
0.2132
0.0946
0.0394
0.2039
-0.2283
0.3723
-0.0256
0.1639
-0.0473
-0.1023
-0.0345
-0.0636
0.1061
0.1947
-0.1641
0.0591
0.0227
0.02
0.2147
-0.0537
0.0396
-20.7347
-10.8418
-9.6253
Refinement TLS group
ID
Refine-ID
Refine TLS-ID
Selection details
1
X-RAY DIFFRACTION
1
chain 'A' and (resid406through453 )
2
X-RAY DIFFRACTION
2
chain 'A' and (resid454through549 )
3
X-RAY DIFFRACTION
3
chain 'A' and (resid550through626 )
4
X-RAY DIFFRACTION
4
chain 'A' and (resid627through671 )
5
X-RAY DIFFRACTION
5
chain 'B' and (resid411through466 )
6
X-RAY DIFFRACTION
6
chain 'B' and (resid467through530 )
7
X-RAY DIFFRACTION
7
chain 'B' and (resid531through575 )
8
X-RAY DIFFRACTION
8
chain 'B' and (resid576through671 )
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