.022841 .013188 0.000000 0.000000 .026375 0.000000 0.000000 0.000000 .009087 0.00000 0.00000 0.00000 RESIDUE LYS 80 AND TML 2 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 4 ABOVE. RESIDUE LYS 94 AND TML 3 FORM EPSILON-N-TRIMETHYLLYSINE. SEE REMARK 4 ABOVE. Ochi, H. Hata, Y. Tanaka, N. Kakudo, M. Sakurai, T. Aihara, S. Morita, Y. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 6 90.00 90.00 120.00 43.780 43.780 110.050 C2 H4 O 44.053 ACETYL GROUP non-polymer C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C34 H34 Fe N4 O4 618.503 HEME C non-polymer C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C9 H21 N2 O2 1 189.275 n N-TRIMETHYLLYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking UK J.Mol.Biol. JMOBAK 0070 0022-2836 166 407 418 10.1016/S0022-2836(83)80092-8 6304326 Structure of rice ferricytochrome c at 2.0 A resolution. 1983 JA J.Biochem.(Tokyo) JOBIAO 0418 0021-924X 87 249 Amino Acid Sequence of Cytochrome C from Rice 1980 UK J.Mol.Biol. JMOBAK 0070 0022-2836 71 807 A Preliminary Crystallographic Investigation of Rice Cytochrome C 1972 JA Agric.Biol.Chem. ABCHA6 0137 0002-1369 32 441 Studies on Respiratory Enzymes in Rice Kernel. Part I. Isolation and Purification of Cytochrome C and Peroxidase 556 from Rice Embryo 1968 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 12267.986 CYTOCHROME C 1 man polymer 618.503 HEME C 1 syn non-polymer 18.015 water 46 nat water no yes (ACE)ASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEENTLYDY LLNP(M3L)KYIPGTKMVFPGL(M3L)KPQERADLISYLKEATS XASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTADKNMAVIWEENTLYDYLLNP KKYIPGTKMVFPGLKKPQERADLISYLKEATS A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n rice Oryza sample 4530 Oryza sativa 2.50 50.74 pdbx_database_status struct_conf struct_conf_type atom_site chem_comp entity pdbx_entity_nonpoly pdbx_nonpoly_scheme pdbx_struct_conn_angle struct_conn struct_ref_seq_dif struct_site repository Initial release Version format compliance Version format compliance Derived calculations Other Atomic model Data collection Database references Derived calculations Non-polymer description Structure summary 1 0 1983-04-21 1 1 2008-03-21 1 2 2011-07-13 1 3 2017-11-29 2 0 2021-03-03 _pdbx_database_status.process_site _atom_site.B_iso_or_equiv _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.type_symbol _chem_comp.formula _chem_comp.formula_weight _chem_comp.id _chem_comp.name _chem_comp.pdbx_synonyms _entity.formula_weight _entity.pdbx_description _pdbx_entity_nonpoly.comp_id _pdbx_entity_nonpoly.name _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_struct_conn_angle.ptnr1_auth_comp_id _pdbx_struct_conn_angle.ptnr1_label_comp_id _pdbx_struct_conn_angle.ptnr2_auth_comp_id _pdbx_struct_conn_angle.ptnr2_label_comp_id _pdbx_struct_conn_angle.ptnr3_auth_comp_id _pdbx_struct_conn_angle.ptnr3_label_comp_id _struct_conn.conn_type_id _struct_conn.id _struct_conn.pdbx_dist_value _struct_conn.pdbx_leaving_atom_flag _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_ref_seq_dif.details _struct_site.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y BNL 1983-03-14 REL REL HEC HEME C HOH water HEM 1 2 HEC HEC 112 A HOH 4 3 HOH HOH 113 A HOH 5 3 HOH HOH 114 A HOH 6 3 HOH HOH 115 A HOH 7 3 HOH HOH 116 A HOH 8 3 HOH HOH 117 A HOH 9 3 HOH HOH 118 A HOH 10 3 HOH HOH 119 A HOH 11 3 HOH HOH 120 A HOH 12 3 HOH HOH 121 A HOH 13 3 HOH HOH 122 A HOH 14 3 HOH HOH 123 A HOH 15 3 HOH HOH 124 A HOH 16 3 HOH HOH 125 A HOH 17 3 HOH HOH 126 A HOH 18 3 HOH HOH 127 A HOH 19 3 HOH HOH 128 A HOH 20 3 HOH HOH 129 A HOH 21 3 HOH HOH 130 A HOH 22 3 HOH HOH 131 A HOH 23 3 HOH HOH 132 A HOH 24 3 HOH HOH 133 A HOH 25 3 HOH HOH 134 A HOH 26 3 HOH HOH 135 A HOH 27 3 HOH HOH 136 A HOH 28 3 HOH HOH 137 A HOH 29 3 HOH HOH 138 A HOH 30 3 HOH HOH 139 A HOH 31 3 HOH HOH 140 A HOH 32 3 HOH HOH 141 A HOH 33 3 HOH HOH 142 A HOH 34 3 HOH HOH 143 A HOH 35 3 HOH HOH 144 A HOH 36 3 HOH HOH 145 A HOH 37 3 HOH HOH 146 A HOH 38 3 HOH HOH 147 A HOH 39 3 HOH HOH 148 A HOH 40 3 HOH HOH 149 A HOH 41 3 HOH HOH 150 A HOH 42 3 HOH HOH 151 A HOH 43 3 HOH HOH 152 A HOH 44 3 HOH HOH 153 A HOH 45 3 HOH HOH 154 A HOH 46 3 HOH HOH 155 A HOH 47 3 HOH HOH 156 A HOH 48 3 HOH HOH 157 A HOH 49 3 HOH HOH 158 A ACE 0 n 1 ACE 0 A ALA 1 n 2 ALA 1 A SER 2 n 3 SER 2 A PHE 3 n 4 PHE 3 A SER 4 n 5 SER 4 A GLU 5 n 6 GLU 5 A ALA 6 n 7 ALA 6 A PRO 7 n 8 PRO 7 A PRO 8 n 9 PRO 8 A GLY 9 n 10 GLY 9 A ASN 10 n 11 ASN 10 A PRO 11 n 12 PRO 11 A LYS 12 n 13 LYS 12 A ALA 13 n 14 ALA 13 A GLY 14 n 15 GLY 14 A GLU 15 n 16 GLU 15 A LYS 16 n 17 LYS 16 A ILE 17 n 18 ILE 17 A PHE 18 n 19 PHE 18 A LYS 19 n 20 LYS 19 A THR 20 n 21 THR 20 A LYS 21 n 22 LYS 21 A CYS 22 n 23 CYS 22 A ALA 23 n 24 ALA 23 A GLN 24 n 25 GLN 24 A CYS 25 n 26 CYS 25 A HIS 26 n 27 HIS 26 A THR 27 n 28 THR 27 A VAL 28 n 29 VAL 28 A ASP 29 n 30 ASP 29 A LYS 30 n 31 LYS 30 A GLY 31 n 32 GLY 31 A ALA 32 n 33 ALA 32 A GLY 33 n 34 GLY 33 A HIS 34 n 35 HIS 34 A LYS 35 n 36 LYS 35 A GLN 36 n 37 GLN 36 A GLY 37 n 38 GLY 37 A PRO 38 n 39 PRO 38 A ASN 39 n 40 ASN 39 A LEU 40 n 41 LEU 40 A ASN 41 n 42 ASN 41 A GLY 42 n 43 GLY 42 A LEU 43 n 44 LEU 43 A PHE 44 n 45 PHE 44 A GLY 45 n 46 GLY 45 A ARG 46 n 47 ARG 46 A GLN 47 n 48 GLN 47 A SER 48 n 49 SER 48 A GLY 49 n 50 GLY 49 A THR 50 n 51 THR 50 A THR 51 n 52 THR 51 A PRO 52 n 53 PRO 52 A GLY 53 n 54 GLY 53 A TYR 54 n 55 TYR 54 A SER 55 n 56 SER 55 A TYR 56 n 57 TYR 56 A SER 57 n 58 SER 57 A THR 58 n 59 THR 58 A ALA 59 n 60 ALA 59 A ASP 60 n 61 ASP 60 A LYS 61 n 62 LYS 61 A ASN 62 n 63 ASN 62 A MET 63 n 64 MET 63 A ALA 64 n 65 ALA 64 A VAL 65 n 66 VAL 65 A ILE 66 n 67 ILE 66 A TRP 67 n 68 TRP 67 A GLU 68 n 69 GLU 68 A GLU 69 n 70 GLU 69 A ASN 70 n 71 ASN 70 A THR 71 n 72 THR 71 A LEU 72 n 73 LEU 72 A TYR 73 n 74 TYR 73 A ASP 74 n 75 ASP 74 A TYR 75 n 76 TYR 75 A LEU 76 n 77 LEU 76 A LEU 77 n 78 LEU 77 A ASN 78 n 79 ASN 78 A PRO 79 n 80 PRO 79 A LYS 80 n 81 M3L 80 A LYS 81 n 82 LYS 81 A TYR 82 n 83 TYR 82 A ILE 83 n 84 ILE 83 A PRO 84 n 85 PRO 84 A GLY 85 n 86 GLY 85 A THR 86 n 87 THR 86 A LYS 87 n 88 LYS 87 A MET 88 n 89 MET 88 A VAL 89 n 90 VAL 89 A PHE 90 n 91 PHE 90 A PRO 91 n 92 PRO 91 A GLY 92 n 93 GLY 92 A LEU 93 n 94 LEU 93 A LYS 94 n 95 M3L 94 A LYS 95 n 96 LYS 95 A PRO 96 n 97 PRO 96 A GLN 97 n 98 GLN 97 A GLU 98 n 99 GLU 98 A ARG 99 n 100 ARG 99 A ALA 100 n 101 ALA 100 A ASP 101 n 102 ASP 101 A LEU 102 n 103 LEU 102 A ILE 103 n 104 ILE 103 A SER 104 n 105 SER 104 A TYR 105 n 106 TYR 105 A LEU 106 n 107 LEU 106 A LYS 107 n 108 LYS 107 A GLU 108 n 109 GLU 108 A ALA 109 n 110 ALA 109 A THR 110 n 111 THR 110 A SER 111 n 112 SER 111 A author_defined_assembly 1 monomeric A HIS 26 A NE2 HIS 27 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B NA HEC 1_555 91.3 A HIS 26 A NE2 HIS 27 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B NB HEC 1_555 86.1 A HEC 112 B NA HEC 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B NB HEC 1_555 91.3 A HIS 26 A NE2 HIS 27 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B NC HEC 1_555 85.7 A HEC 112 B NA HEC 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B NC HEC 1_555 176.7 A HEC 112 B NB HEC 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B NC HEC 1_555 89.9 A HIS 26 A NE2 HIS 27 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B ND HEC 1_555 90.2 A HEC 112 B NA HEC 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B ND HEC 1_555 90.5 A HEC 112 B NB HEC 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B ND HEC 1_555 175.9 A HEC 112 B NC HEC 1_555 A HEC 112 B FE HEC 1_555 A HEC 112 B ND HEC 1_555 88.1 A HIS 26 A NE2 HIS 27 1_555 A HEC 112 B FE HEC 1_555 A MET 88 A SD MET 89 1_555 178.3 A HEC 112 B NA HEC 1_555 A HEC 112 B FE HEC 1_555 A MET 88 A SD MET 89 1_555 88.7 A HEC 112 B NB HEC 1_555 A HEC 112 B FE HEC 1_555 A MET 88 A SD MET 89 1_555 95.6 A HEC 112 B NC HEC 1_555 A HEC 112 B FE HEC 1_555 A MET 88 A SD MET 89 1_555 94.3 A HEC 112 B ND HEC 1_555 A HEC 112 B FE HEC 1_555 A MET 88 A SD MET 89 1_555 88.1 A M3L 80 N-TRIMETHYLLYSINE A M3L 81 LYS A M3L 94 N-TRIMETHYLLYSINE A M3L 95 LYS 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 1 A ARG 46 0.149 SIDE CHAIN 1 15.74 2.20 113.40 129.14 A A A CA CB CG GLU GLU GLU 5 5 5 N 1 15.68 2.20 113.40 129.08 A A A CA CB CG LYS LYS LYS 12 12 12 N 1 -11.13 1.10 119.40 108.27 A A A NH1 CZ NH2 ARG ARG ARG 46 46 46 N 1 6.94 0.50 120.30 127.24 A A A NE CZ NH1 ARG ARG ARG 46 46 46 N 1 3.05 0.50 120.30 123.35 A A A NE CZ NH2 ARG ARG ARG 46 46 46 N 1 12.10 2.00 118.30 130.40 A A A CG CD OE1 GLU GLU GLU 68 68 68 N 1 22.93 2.10 111.80 134.73 A A A CG CD NE ARG ARG ARG 99 99 99 N 1 33.37 1.40 123.60 156.97 A A A CD NE CZ ARG ARG ARG 99 99 99 N 1 4.90 0.50 120.30 125.20 A A A NE CZ NH1 ARG ARG ARG 99 99 99 N 1 -8.67 0.50 120.30 111.63 A A A NE CZ NH2 ARG ARG ARG 99 99 99 N 1 13.70 2.20 113.40 127.10 A A A CA CB CG GLU GLU GLU 108 108 108 N 1 16.77 2.70 114.20 130.97 A A A CB CG CD GLU GLU GLU 108 108 108 N 1 A A CD NE ARG ARG 99 99 -0.158 0.017 1.460 1.302 N 1 A A CE O MET HOH 63 118 1.23 1_555 6_555 1 A A O O HOH HOH 128 133 2.04 1_555 6_665 1 A LYS 35 -131.68 -143.07 1 A ASN 78 -166.77 86.27 0.1900000 1.5 1 1.5 46 953 49 0 858 0.02 CYTOCHROME C STRUCTURE OF RICE FERRICYTOCHROME C AT 2.0 ANGSTROMS RESOLUTION 1 N N 2 N N 3 N N A ASN 10 A ASN 11 HELX_P A CYS 22 A CYS 23 1 H1 13 A SER 57 A SER 58 HELX_P A MET 63 A MET 64 1 H2 7 A GLU 68 A GLU 69 HELX_P A ASN 78 A ASN 79 1 H3 11 A ASN 78 A ASN 79 HELX_P A ILE 83 A ILE 84 1 H4 6 A LYS 95 A LYS 96 HELX_P A SER 111 A SER 112 1 H5 17 covale 1.335 both A ACE 0 A C ACE 1 1_555 A ALA 1 A N ALA 2 1_555 covale 1.914 none A CYS 22 A SG CYS 23 1_555 A HEC 112 B CAB HEC 1_555 covale 1.965 none A CYS 25 A SG CYS 26 1_555 A HEC 112 B CAC HEC 1_555 covale 1.295 both A PRO 79 A C PRO 80 1_555 A M3L 80 A N M3L 81 1_555 covale 1.311 both A M3L 80 A C M3L 81 1_555 A LYS 81 A N LYS 82 1_555 covale 1.300 both A LEU 93 A C LEU 94 1_555 A M3L 94 A N M3L 95 1_555 covale 1.311 both A M3L 94 A C M3L 95 1_555 A LYS 95 A N LYS 96 1_555 metalc 2.037 A HIS 26 A NE2 HIS 27 1_555 A HEC 112 B FE HEC 1_555 metalc 2.351 A MET 88 A SD MET 89 1_555 A HEC 112 B FE HEC 1_555 ELECTRON TRANSPORT(CYTOCHROME) ELECTRON TRANSPORT(CYTOCHROME) CYC_ORYSA UNP 1 1 P00055 ASFSEAPPGNPKAGEKIFKTKCAQCHTVDKGAGHKQGPNLNGLFGRQSGTTPGYSYSTANKNMAVIWEENTLYDYLLNPK KYIPGTKMVFPGLKKPQERADLISYLKEATS 1 111 1CCR 1 111 P00055 A 1 2 112 1 ASN conflict ASP 60 1CCR A P00055 UNP 60 61 BINDING SITE FOR RESIDUE HEC A 112 A HEC 112 Software 23 A LYS 21 A LYS 22 23 1_555 A CYS 22 A CYS 23 23 1_555 A CYS 25 A CYS 26 23 1_555 A HIS 26 A HIS 27 23 1_555 A GLN 36 A GLN 37 23 1_555 A GLY 37 A GLY 38 23 1_555 A PRO 38 A PRO 39 23 1_555 A SER 48 A SER 49 23 1_555 A GLY 49 A GLY 50 23 1_555 A TYR 54 A TYR 55 23 1_555 A TYR 56 A TYR 57 23 1_555 A SER 57 A SER 58 23 1_555 A ASP 60 A ASP 61 23 1_555 A TRP 67 A TRP 68 23 1_555 A TYR 75 A TYR 76 23 1_555 A THR 86 A THR 87 23 1_555 A LYS 87 A LYS 88 23 1_555 A MET 88 A MET 89 23 1_555 A VAL 89 A VAL 90 23 1_555 A PHE 90 A PHE 91 23 1_555 A LEU 102 A LEU 103 23 1_555 A HOH 123 C HOH 23 1_555 A HOH 135 C HOH 23 1_555 169 P 61