The PKA system is simple enough that there is no need to split up the PDB model file from Step 1 into several pieces. The modified model file is:
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Label: CAMP-Dependent Protein Kinase (A and I chains only with water)
Entities:
- Label: A
Components: [LYS.8, GLY.9, SER.10, GLU.11, GLN.12, GLU.13, SER.14, VAL.15, LYS.16,
GLU.17, PHE.18, LEU.19, ALA.20, LYS.21, ALA.22, LYS.23, GLU.24, ASP.25, PHE.26,
LEU.27, LYS.28, LYS.29, TRP.30, GLU.31, ASN.32, PRO.33, ALA.34, GLN.35, ASN.36,
THR.37, ALA.38, HIS.39, LEU.40, ASP.41, GLN.42, PHE.43, GLU.44, ARG.45, ILE.46,
LYS.47, THR.48, LEU.49, GLY.50, THR.51, GLY.52, SER.53, PHE.54, GLY.55, ARG.56,
VAL.57, MET.58, LEU.59, VAL.60, LYS.61, HIS.62, LYS.63, GLU.64, THR.65, GLY.66,
ASN.67, HIS.68, PHE.69, ALA.70, MET.71, LYS.72, ILE.73, LEU.74, ASP.75, LYS.76,
GLN.77, LYS.78, VAL.79, VAL.80, LYS.81, LEU.82, LYS.83, GLN.84, ILE.85, GLU.86,
HIS.87, THR.88, LEU.89, ASN.90, GLU.91, LYS.92, ARG.93, ILE.94, LEU.95, GLN.96,
ALA.97, VAL.98, ASN.99, PHE.100, PRO.101, PHE.102, LEU.103, VAL.104, LYS.105,
LEU.106, GLU.107, TYR.108, SER.109, PHE.110, LYS.111, ASP.112, ASN.113, SER.114,
ASN.115, LEU.116, TYR.117, MET.118, VAL.119, MET.120, GLU.121, TYR.122, VAL.123,
PRO.124, GLY.125, GLY.126, GLU.127, MET.128, PHE.129, SER.130, HIS.131, LEU.132,
ARG.133, ARG.134, ILE.135, GLY.136, ARG.137, PHE.138, SER.139, GLU.140, PRO.141,
HIS.142, ALA.143, ARG.144, PHE.145, TYR.146, ALA.147, ALA.148, GLN.149, ILE.150,
VAL.151, LEU.152, THR.153, PHE.154, GLU.155, TYR.156, LEU.157, HIS.158, SER.159,
LEU.160, ASP.161, LEU.162, ILE.163, TYR.164, ARG.165, ASP.166, LEU.167, LYS.168,
PRO.169, GLU.170, ASN.171, LEU.172, LEU.173, ILE.174, ASP.175, GLN.176, GLN.177,
GLY.178, TYR.179, ILE.180, GLN.181, VAL.182, THR.183, ASP.184, PHE.185, GLY.186,
PHE.187, ALA.188, LYS.189, ARG.190, VAL.191, LYS.192, GLY.193, ARG.194, THR.195,
TRP.196, TPO.197, LEU.198, CYS.199, GLY.200, THR.201, PRO.202, GLU.203, TYR.204,
LEU.205, ALA.206, PRO.207, GLU.208, ILE.209, ILE.210, LEU.211, SER.212, LYS.213,
GLY.214, TYR.215, ASN.216, LYS.217, ALA.218, VAL.219, ASP.220, TRP.221, TRP.222,
ALA.223, LEU.224, GLY.225, VAL.226, LEU.227, ILE.228, TYR.229, GLU.230, MET.231,
ALA.232, ALA.233, GLY.234, TYR.235, PRO.236, PRO.237, PHE.238, PHE.239, ALA.240,
ASP.241, GLN.242, PRO.243, ILE.244, GLN.245, ILE.246, TYR.247, GLU.248, LYS.249,
ILE.250, VAL.251, SER.252, GLY.253, LYS.254, VAL.255, ARG.256, PHE.257, PRO.258,
SER.259, HIS.260, PHE.261, SER.262, SER.263, ASP.264, LEU.265, LYS.266, ASP.267,
LEU.268, LEU.269, ARG.270, ASN.271, LEU.272, LEU.273, GLN.274, VAL.275, ASP.276,
LEU.277, THR.278, LYS.279, ARG.280, PHE.281, GLY.282, ASN.283, LEU.284, LYS.285,
ASP.286, GLY.287, VAL.288, ASN.289, ASP.290, ILE.291, LYS.292, ASN.293, HIS.294,
LYS.295, TRP.296, PHE.297, ALA.298, THR.299, THR.300, ASP.301, TRP.302, ILE.303,
ALA.304, ILE.305, TYR.306, GLN.307, ARG.308, LYS.309, VAL.310, GLU.311, ALA.312,
PRO.313, PHE.314, ILE.315, PRO.316, LYS.317, PHE.318, LYS.319, GLY.320, PRO.321,
GLY.322, ASP.323, THR.324, SER.325, ASN.326, PHE.327, ASP.328, ASP.329, TYR.330,
GLU.331, GLU.332, GLU.333, GLU.334, ILE.335, ARG.336, VAL.337, SER.338, ILE.339,
ASN.340, GLU.341, LYS.342, CYS.343, GLY.344, LYS.345, GLU.346, PHE.347, SER.348,
GLU.349, PHE.350, MG.401, MG.402, ATP.400, HOH.404, HOH.405, HOH.406,
HOH.407, HOH.408, HOH.409, HOH.410, HOH.411, HOH.412, HOH.413, HOH.414, HOH.415,
HOH.416, HOH.417, HOH.418, HOH.419, HOH.420, HOH.421, HOH.422, HOH.423, HOH.424,
HOH.425, HOH.426, HOH.427, HOH.428, HOH.429, HOH.430, HOH.431, HOH.432, HOH.433,
HOH.434, HOH.435, HOH.436, HOH.437, HOH.438, HOH.439, HOH.440, HOH.441, HOH.442,
HOH.443, HOH.444, HOH.445, HOH.446, HOH.447, HOH.448, HOH.449, HOH.450, HOH.451,
HOH.452, HOH.453, HOH.454, HOH.455, HOH.456, HOH.457, HOH.458, HOH.459, HOH.460,
HOH.461, HOH.462, HOH.463, HOH.464, HOH.465, HOH.466, HOH.467, HOH.468, HOH.469,
HOH.470, HOH.471, HOH.472, HOH.473, HOH.474, HOH.475, HOH.476, HOH.477, HOH.478,
HOH.479, HOH.480, HOH.481, HOH.482, HOH.483, HOH.484, HOH.485, HOH.486, HOH.487,
HOH.488, HOH.489, HOH.490, HOH.491, HOH.492, HOH.493, HOH.494, HOH.495, HOH.496,
HOH.497, HOH.498, HOH.499, HOH.500, HOH.501, HOH.502, HOH.503, HOH.504, HOH.505,
HOH.506, HOH.507, HOH.508, HOH.509, HOH.510, HOH.511, HOH.512, HOH.513, HOH.514,
HOH.515, HOH.516, HOH.517, HOH.518, HOH.519, HOH.520, HOH.521, HOH.522, HOH.523,
HOH.524, HOH.525, HOH.526, HOH.527, HOH.528, HOH.529, HOH.530, HOH.531, HOH.532]
Variants:
- Label : Epsilon_Protonated
Component : HIS.39
- Label : Epsilon_Protonated
Component : HIS.62
- Label : Doubly_Protonated
Component : HIS.87
- Label : Epsilon_Protonated
Component : HIS.131
- Label : Epsilon_Protonated
Component : HIS.294
- Label: I
Components: [THR.1, THR.2, TYR.3, ALA.4, ASP.5, PHE.6, ILE.7, ALA.8, SER.9, GLY.10,
ARG.11, THR.12, GLY.13, ARG.14, ARG.15, ASN.16, SER.17, ILE.18, HIS.19, ASP.20,
HOH.49, HOH.54, HOH.63, HOH.70, HOH.73, HOH.74, HOH.75, HOH.76, HOH.77, HOH.78,
HOH.79, HOH.88, HOH.109, HOH.110, HOH.111, HOH.113, HOH.129, HOH.146, HOH.147,
HOH.148]
Variants:
- Label : Epsilon_Protonated
Component : HIS.19
Linear Polymers:
- { Left Terminal Component: 'A:LYS.8', Right Terminal Component: 'A:PHE.350'}
- { Left Terminal Component: 'I:THR.1', Right Terminal Component: 'I:ASP.20' }
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