0.029593 -0.000001 -0.000001 0.000000 0.013007 0.000000 0.000000 0.000000 0.013237 0.00000 0.00000 0.00000 Jacobs, S.A. Khorasanizadeh, S. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 8 90.00 90.00 90.00 33.792 76.883 75.548 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 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 C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C8 H18 N2 O2 174.241 n N-DIMETHYL-LYSINE 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 US Science SCIEAS 0038 0036-8075 295 2080 2083 10.1126/science.1069473 11859155 Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. 2002 10.2210/pdb1kna/pdb pdb_00001kna 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 100 1 CCD 2001-10-10 BRUKER SMART 6000 SINGLE WAVELENGTH M x-ray 1 1.54 1.0 1.54 ROTATING ANODE RIGAKU 8586.468 HETEROCHROMATIN PROTEIN 1 Residues 23-76 K38M 1 man polymer 1756.017 METHYLATED Histone H3 Residues 1-16 P16Y 1 syn polymer 18.015 water 86 nat water HP1, NONHISTONE CHROMOSOMAL PROTEIN C1A9 ANTIGEN no no MKKHHHHHHAEEEEEEYAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD MKKHHHHHHAEEEEEEYAVEKIIDRRVRKGMVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD A polypeptide(L) no yes ARTKQTAR(MLY)STGGKAY ARTKQTARKSTGGKAY P 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 fruit fly Drosophila Escherichia sample 7227 Drosophila melanogaster 562 Escherichia coli BL21(De3)pLysS Plasmid pET11a 1 2.37 48.14 VAPOR DIFFUSION, SITTING DROP 6.0 Ammonium Sulfate, MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 283.0K 283.0 database_2 struct_conn struct_ref_seq_dif repository Initial release Version format compliance Version format compliance Database references Derived calculations 1 0 2002-03-20 1 1 2008-04-27 1 2 2011-07-13 1 3 2021-10-27 _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_conn.pdbx_leaving_atom_flag _struct_ref_seq_dif.details RCSB Y RCSB 2001-12-18 REL REL HOH water Synthetic peptide Corresponding to residues 1-16 of Histone H3. K9 dimethylated. P16Y mutation. sample HOH 1 3 HOH HOH 77 A HOH 2 3 HOH HOH 78 A HOH 3 3 HOH HOH 79 A HOH 4 3 HOH HOH 80 A HOH 5 3 HOH HOH 81 A HOH 6 3 HOH HOH 82 A HOH 7 3 HOH HOH 83 A HOH 8 3 HOH HOH 84 A HOH 9 3 HOH HOH 85 A HOH 10 3 HOH HOH 86 A HOH 11 3 HOH HOH 87 A HOH 12 3 HOH HOH 88 A HOH 13 3 HOH HOH 89 A HOH 14 3 HOH HOH 90 A HOH 15 3 HOH HOH 91 A HOH 16 3 HOH HOH 92 A HOH 17 3 HOH HOH 93 A HOH 18 3 HOH HOH 94 A HOH 19 3 HOH HOH 95 A HOH 20 3 HOH HOH 96 A HOH 22 3 HOH HOH 97 A HOH 23 3 HOH HOH 98 A HOH 25 3 HOH HOH 99 A HOH 26 3 HOH HOH 100 A HOH 27 3 HOH HOH 101 A HOH 28 3 HOH HOH 102 A HOH 29 3 HOH HOH 103 A HOH 30 3 HOH HOH 104 A HOH 31 3 HOH HOH 105 A HOH 32 3 HOH HOH 106 A HOH 33 3 HOH HOH 107 A HOH 34 3 HOH HOH 108 A HOH 36 3 HOH HOH 109 A HOH 37 3 HOH HOH 110 A HOH 38 3 HOH HOH 111 A HOH 39 3 HOH HOH 112 A HOH 40 3 HOH HOH 113 A HOH 41 3 HOH HOH 114 A HOH 42 3 HOH HOH 115 A HOH 43 3 HOH HOH 116 A HOH 44 3 HOH HOH 117 A HOH 45 3 HOH HOH 118 A HOH 46 3 HOH HOH 119 A HOH 47 3 HOH HOH 120 A HOH 49 3 HOH HOH 121 A HOH 50 3 HOH HOH 122 A HOH 51 3 HOH HOH 123 A HOH 52 3 HOH HOH 124 A HOH 53 3 HOH HOH 125 A HOH 54 3 HOH HOH 126 A HOH 55 3 HOH HOH 127 A HOH 56 3 HOH HOH 128 A HOH 57 3 HOH HOH 129 A HOH 58 3 HOH HOH 130 A HOH 59 3 HOH HOH 131 A HOH 60 3 HOH HOH 132 A HOH 61 3 HOH HOH 133 A HOH 62 3 HOH HOH 134 A HOH 63 3 HOH HOH 135 A HOH 64 3 HOH HOH 136 A HOH 65 3 HOH HOH 137 A HOH 66 3 HOH HOH 138 A HOH 67 3 HOH HOH 139 A HOH 68 3 HOH HOH 140 A HOH 69 3 HOH HOH 141 A HOH 71 3 HOH HOH 142 A HOH 72 3 HOH HOH 143 A HOH 73 3 HOH HOH 144 A HOH 74 3 HOH HOH 145 A HOH 75 3 HOH HOH 146 A HOH 78 3 HOH HOH 147 A HOH 79 3 HOH HOH 148 A HOH 80 3 HOH HOH 149 A HOH 81 3 HOH HOH 150 A HOH 82 3 HOH HOH 151 A HOH 83 3 HOH HOH 152 A HOH 21 3 HOH HOH 21 P HOH 24 3 HOH HOH 24 P HOH 35 3 HOH HOH 35 P HOH 48 3 HOH HOH 48 P HOH 70 3 HOH HOH 70 P HOH 76 3 HOH HOH 76 P HOH 77 3 HOH HOH 77 P HOH 84 3 HOH HOH 84 P HOH 85 3 HOH HOH 85 P HOH 86 3 HOH HOH 86 P n 1 8 A n 2 9 A n 3 10 A n 4 11 A n 5 12 A n 6 13 A n 7 14 A n 8 15 A n 9 16 A n 10 17 A n 11 18 A n 12 19 A n 13 20 A n 14 21 A n 15 22 A GLU 23 n 16 GLU 23 A TYR 24 n 17 TYR 24 A ALA 25 n 18 ALA 25 A VAL 26 n 19 VAL 26 A GLU 27 n 20 GLU 27 A LYS 28 n 21 LYS 28 A ILE 29 n 22 ILE 29 A ILE 30 n 23 ILE 30 A ASP 31 n 24 ASP 31 A ARG 32 n 25 ARG 32 A ARG 33 n 26 ARG 33 A VAL 34 n 27 VAL 34 A ARG 35 n 28 ARG 35 A LYS 36 n 29 LYS 36 A GLY 37 n 30 GLY 37 A MET 38 n 31 MET 38 A VAL 39 n 32 VAL 39 A GLU 40 n 33 GLU 40 A TYR 41 n 34 TYR 41 A TYR 42 n 35 TYR 42 A LEU 43 n 36 LEU 43 A LYS 44 n 37 LYS 44 A TRP 45 n 38 TRP 45 A LYS 46 n 39 LYS 46 A GLY 47 n 40 GLY 47 A TYR 48 n 41 TYR 48 A PRO 49 n 42 PRO 49 A GLU 50 n 43 GLU 50 A THR 51 n 44 THR 51 A GLU 52 n 45 GLU 52 A ASN 53 n 46 ASN 53 A THR 54 n 47 THR 54 A TRP 55 n 48 TRP 55 A GLU 56 n 49 GLU 56 A PRO 57 n 50 PRO 57 A GLU 58 n 51 GLU 58 A ASN 59 n 52 ASN 59 A ASN 60 n 53 ASN 60 A LEU 61 n 54 LEU 61 A ASP 62 n 55 ASP 62 A CYS 63 n 56 CYS 63 A GLN 64 n 57 GLN 64 A ASP 65 n 58 ASP 65 A LEU 66 n 59 LEU 66 A ILE 67 n 60 ILE 67 A GLN 68 n 61 GLN 68 A GLN 69 n 62 GLN 69 A TYR 70 n 63 TYR 70 A GLU 71 n 64 GLU 71 A ALA 72 n 65 ALA 72 A SER 73 n 66 SER 73 A ARG 74 n 67 ARG 74 A n 68 75 A n 69 76 A n 1 1 P n 2 2 P n 3 3 P n 4 4 P GLN 5 n 5 GLN 5 P THR 6 n 6 THR 6 P ALA 7 n 7 ALA 7 P ARG 8 n 8 ARG 8 P MLY 9 n 9 MLY 9 P SER 10 n 10 SER 10 P n 11 11 P n 12 12 P n 13 13 P n 14 14 P n 15 15 P n 16 16 P author_and_software_defined_assembly PISA 2 dimeric 1030 -4 4040 P MLY 9 N-DIMETHYL-LYSINE B MLY 9 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 A O THR 54 A O THR 47 A N LEU 43 A N LEU 36 A O GLU 40 A O GLU 33 A N ARG 33 A N ARG 26 A N TYR 24 A N TYR 17 P O ALA 7 B O ALA 7 P O THR 6 B O THR 6 A N ASP 62 A N ASP 55 1 A HOH 146 C HOH 1 A CG ASN 59 A CG ASN 52 0 Y 1 A OD1 ASN 59 A OD1 ASN 52 0 Y 1 A ND2 ASN 59 A ND2 ASN 52 0 Y 1 A MET 8 A MET 1 1 Y 1 A LYS 9 A LYS 2 1 Y 1 A LYS 10 A LYS 3 1 Y 1 A HIS 11 A HIS 4 1 Y 1 A HIS 12 A HIS 5 1 Y 1 A HIS 13 A HIS 6 1 Y 1 A HIS 14 A HIS 7 1 Y 1 A HIS 15 A HIS 8 1 Y 1 A HIS 16 A HIS 9 1 Y 1 A ALA 17 A ALA 10 1 Y 1 A GLU 18 A GLU 11 1 Y 1 A GLU 19 A GLU 12 1 Y 1 A GLU 20 A GLU 13 1 Y 1 A GLU 21 A GLU 14 1 Y 1 A GLU 22 A GLU 15 1 Y 1 A LYS 75 A LYS 68 1 Y 1 A ASP 76 A ASP 69 1 Y 1 P ALA 1 B ALA 1 1 Y 1 P ARG 2 B ARG 2 1 Y 1 P THR 3 B THR 3 1 Y 1 P LYS 4 B LYS 4 1 Y 1 P THR 11 B THR 11 1 Y 1 P GLY 12 B GLY 12 1 Y 1 P GLY 13 B GLY 13 1 Y 1 P LYS 14 B LYS 14 1 Y 1 P ALA 15 B ALA 15 1 Y 1 P TYR 16 B TYR 16 1 Y 1 A A O O HOH HOH 147 147 1.27 1_555 3_555 1 A A OG OG SER SER 73 73 1.74 1_555 4_565 26.3 5.6 -3.48 -2.11 0.00 0.00 0.00 0.259 0.026 0.228 2.10 28.63 654 6008 5354 10.90 99.80 RANDOM 117307.12 1 THROUGHOUT 0.00 MOLECULAR REPLACEMENT Engh & Huber 0.32 0.26 5.00 0.19 0.16 2.10 28.63 86 585 0 0 499 0.005 1.2 22.8 0.59 0.281 0.026 0.245 2.23 116 842 6 12.1 99.30 14.8 2.10 30.0 1KNA 6032 6032 2.0 0.0 0.079 1 61.6 20.1 99.8 2.10 2.23 10.5 842 0.279 99.3 data reduction DENZO data reduction TRUNCATE refinement CNS data scaling CCP4 (TRUNCATE) phasing CNS Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9. 1 N N 2 N N 3 N N 3 N N A PRO 49 A PRO 42 HELX_P A ASN 53 A ASN 46 5 1 5 A CYS 63 A CYS 56 HELX_P A ARG 74 A ARG 67 1 2 12 covale 1.325 both P ARG 8 B C ARG 8 1_555 P MLY 9 B N MLY 9 1_555 covale 1.329 both P MLY 9 B C MLY 9 1_555 P SER 10 B N SER 10 1_555 STRUCTURAL PROTEIN chromo, HP1, histone, dimethyllysine, methyllysine, H3, STRUCTURAL PROTEIN HP1_DROME UNP 1 17 P05205 AEEEEEEYAVEKIIDRRVRKGKVEYYLKWKGYPETENTWEPENNLDCQDLIQQYEASRKD H3_DROME UNP 2 1 P02299 ARTKQTARKSTGGKAP 17 76 1KNA 8 76 P05205 A 1 1 69 1 16 1KNA 1 16 P02299 P 2 1 16 1 engineered mutation MET 8 1KNA A P05205 UNP 8 1 1 engineered mutation LYS 9 1KNA A P05205 UNP 9 2 1 engineered mutation LYS 10 1KNA A P05205 UNP 10 3 1 expression tag HIS 11 1KNA A P05205 UNP 11 4 1 expression tag HIS 12 1KNA A P05205 UNP 12 5 1 expression tag HIS 13 1KNA A P05205 UNP 13 6 1 expression tag HIS 14 1KNA A P05205 UNP 14 7 1 expression tag HIS 15 1KNA A P05205 UNP 15 8 1 expression tag HIS 16 1KNA A P05205 UNP 16 9 1 LYS engineered mutation MET 38 1KNA A P05205 UNP 38 31 2 LYS modified residue MLY 9 1KNA P P02299 UNP 9 9 2 PRO engineered mutation TYR 16 1KNA P P02299 UNP 16 16 5 anti-parallel anti-parallel anti-parallel anti-parallel A THR 54 A THR 47 A PRO 57 A PRO 50 A MET 38 A MET 31 A TRP 45 A TRP 38 A TYR 24 A TYR 17 A ARG 35 A ARG 28 P THR 6 B THR 6 P ALA 7 B ALA 7 A LEU 61 A LEU 54 A ASP 62 A ASP 55 20 C 2 2 21