1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 Clore, G.M. Huth, J.R. Bewley, C. Gronenborn, A.M. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 1 90.00 90.00 90.00 1.000 1.000 1.000 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 C10 H14 N5 O6 P 331.222 y 2'-DEOXYADENOSINE-5'-MONOPHOSPHATE DNA linking C9 H14 N3 O7 P 307.197 y 2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE DNA linking C10 H14 N5 O7 P 347.221 y 2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE DNA linking C10 H15 N2 O8 P 322.208 y THYMIDINE-5'-MONOPHOSPHATE DNA linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H15 N2 O2 1 147.195 y 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 C5 H11 N O2 117.146 y VALINE L-peptide linking US Nat.Struct.Biol. NSBIEW 2024 1072-8368 4 657 665 10.1038/nsb0897-657 9253416 The solution structure of an HMG-I(Y)-DNA complex defines a new architectural minor groove binding motif. 1997 10.2210/pdb2ezd/pdb pdb_00002ezd 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 3662.404 DNA (5'-D(*GP*GP*GP*AP*AP*AP*TP*TP*CP*CP*TP*C)-3') 1 syn polymer 3662.404 DNA (5'-D(*GP*AP*GP*GP*AP*AP*TP*TP*TP*CP*CP*C)-3') 1 syn polymer 2727.262 HIGH MOBILITY GROUP PROTEIN HMG-I/HMG-Y 1 man polymer HIGH MOBILITY GROUP PROTEIN HMG no no (DG)(DG)(DG)(DA)(DA)(DA)(DT)(DT)(DC)(DC)(DT)(DC) GGGAAATTCCTC B polydeoxyribonucleotide no no (DG)(DA)(DG)(DG)(DA)(DA)(DT)(DT)(DT)(DC)(DC)(DC) GAGGAATTTCCC C polydeoxyribonucleotide no no VPTPKRPRGRPKGSKNKGAAKTRKT VPTPKRPRGRPKGSKNKGAAKTRKT 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 human Homo Escherichia sample 9606 Homo sapiens 562 Escherichia coli 3.027 1 19 B 201 C 224 -0.226 B_DG201:DC224_C 1 0.584 -0.504 0.033 -0.190 9.241 1 19 B 202 C 223 -0.935 B_DG202:DC223_C 2 -2.749 -0.190 0.300 -0.022 5.404 1 19 B 203 C 222 -2.266 B_DG203:DC222_C 3 -11.612 0.059 0.371 -0.213 0.034 1 20 B 204 C 221 -4.179 B_DA204:DT221_C 4 -12.391 -0.062 0.515 -0.170 -4.133 1 20 B 205 C 220 -4.307 B_DA205:DT220_C 5 -13.523 0.211 -0.114 -0.203 12.433 1 20 B 206 C 219 -10.661 B_DA206:DT219_C 6 -5.575 -0.187 0.155 -0.056 4.139 1 20 B 207 C 218 -4.326 B_DT207:DA218_C 7 -14.804 -0.027 -0.252 -0.183 -0.429 1 20 B 208 C 217 0.910 B_DT208:DA217_C 8 -16.294 0.240 -0.171 -0.188 -9.655 1 19 B 209 C 216 -0.470 B_DC209:DG216_C 9 -11.591 0.183 0.050 -0.125 -9.334 1 19 B 210 C 215 -2.396 B_DC210:DG215_C 10 -9.423 0.038 -0.274 -0.259 -5.370 1 20 B 211 C 214 -8.928 B_DT211:DA214_C 11 -3.202 0.113 0.116 -0.063 -3.011 1 19 B 212 C 213 1.927 B_DC212:DG213_C 12 0.567 0.485 0.026 -0.171 3.919 36.356 B B 201 202 -6.288 C C 224 223 3.955 -3.915 -0.514 0.304 BB_DG201DG202:DC223DC224_CC 1 -1.483 2.381 36.122 1.146 0.574 4.049 35.632 B B 202 203 0.453 C C 223 222 4.047 0.277 -0.142 0.137 BB_DG202DG203:DC222DC223_CC 2 -0.226 0.369 35.630 0.175 0.192 3.935 35.409 B B 203 204 5.612 C C 222 221 3.943 3.408 -0.149 0.066 BB_DG203DA204:DT221DC222_CC 3 -1.236 2.035 35.229 -0.496 0.026 3.927 35.955 B B 204 205 1.872 C C 221 220 3.938 1.155 -0.203 -0.046 BB_DA204DA205:DT220DT221_CC 4 1.055 -1.709 35.922 -0.272 0.510 2.925 33.243 B B 205 206 -7.080 C C 220 219 2.921 -4.039 -0.324 -0.086 BB_DA205DA206:DT219DT220_CC 5 -1.946 3.411 32.948 0.457 0.275 4.050 34.626 B B 206 207 1.642 C C 219 218 4.049 0.976 0.328 -0.405 BB_DA206DT207:DA218DT219_CC 6 3.010 -5.063 34.485 -0.867 0.024 3.997 38.242 B B 207 208 -7.587 C C 218 217 4.046 -4.957 0.459 0.167 BB_DT207DT208:DA217DA218_CC 7 0.390 -0.597 37.929 1.025 -0.641 4.153 39.152 B B 208 209 -3.607 C C 217 216 4.188 -2.415 -0.134 0.505 BB_DT208DC209:DG216DA217_CC 8 -1.385 2.068 39.057 1.123 -0.012 3.744 37.646 B B 209 210 -9.064 C C 216 215 3.819 -5.827 -0.091 0.198 BB_DC209DC210:DG215DG216_CC 9 0.749 -1.166 37.201 1.186 0.254 3.692 36.311 B B 210 211 -10.722 C C 215 214 3.742 -6.645 -0.423 0.028 BB_DC210DT211:DA214DG215_CC 10 -1.491 2.406 35.688 1.110 0.440 4.008 32.911 B B 211 212 -1.429 C C 214 213 4.015 -0.809 0.857 0.341 BB_DT211DC212:DG213DA214_CC 11 0.092 -0.162 32.901 0.772 -1.493 database_2 pdbx_database_status pdbx_struct_assembly pdbx_struct_oper_list repository Initial release Version format compliance Version format compliance Database references Derived calculations Other 1 0 1997-10-15 1 1 2008-03-24 1 2 2011-07-13 1 3 2022-03-09 _database_2.pdbx_DOI _database_2.pdbx_database_accession _pdbx_database_status.process_site ENSEMBLE OF 35 STRUCTURES Y BNL 1997-06-04 REL DATA WERE RECORDED ON A 2:1 COMPLEX OF DNA DODECAMER TO HMG-I(Y) 50-91 WHICH CONTAINS THE SECOND AND THIRD DNA DNA BINDING DOMAINS. EACH DNA BINDING DOMAIN BINDS TO 1 MOLECULE OF DNA. 35 1 6.1 306 K THE STRUCTURES WERE CALCULATED USING THE SIMULATED ANNEALING PROTOCOL OF NILGES ET AL. (1988) FEBS LETT. 229, 129 - 136 USING THE PROGRAM X-PLOR 3.1 (BRUNGER) MODIFIED TO INCORPORATE COUPLING CONSTANT (GARRETT ET AL. (1984) J. MAGN RESON. SERIES B 104, 99 - 103), CARBON CHEMICAL SHIFT (KUSZEWSKI ET AL. (1995) J. MAGN. RESON. SERIES B 106, 92 - 96) RESTRAINTS AND A CONFORMATIONAL DATABASE POTENTIAL (KUSZEWSKI ET AL. (1996) PROTEIN SCI 5, 1067 - 1080 AND (1997) J. MAGN. RESON. 125, 171-177) THE 3D STRUCTURE OF THE COMPLEX OF THE SECOND DNA BINDING DOMAIN OF HMG-I(Y) COMPLEXED TO DNA WAS SOLVED BY MULTI-DIMENSIONAL HETERONUCLEAR-EDITED AND -FILTERED NMR (A) PROTEIN: 71 SEQUENTIAL (|I-J|=1), 4 MEDIUM RANGE (1 < |I-J| >=5) AND 64 INTRARESIDUE APPROXIMATE INTERPROTON DISTANCE RESTRAINTS; NULL 36 TORSION ANGLE RESTRAINTS 13 THREE-BOND HN-HA AND 8 THREE_BOND COCO COUPLING CONSTANT RESTRAINTS; 39 (21 CALPHA AND 18 CBETA) 13C SHIFT RESTRAINTS. (B) DNA: 249 INTRARESIDUE, 119 SEQUENTIAL INTRASTRAND AND 33 INTERSTRAND INTERPROTON DISTANCE RESTRAINTS; 42 DISTANCES FOR WATSON-CRICK BASE PAIR HYDROGEN BONDS; 136 TORSION ANGLE RESTRAINTS (C) 73 INTERMOLECULAR INTERPROTON DISTANCE RESTRAINTS (D) 5 INTERMOLECULAR DISTANCE RESTRAINTS TO PHOSPHATES (E) 20 'REPULSIVE' RESTRAINTS THE STRUCTURE IN THIS ENTRY IS THE RESTRAINED REGULARIZED MEAN STRUCTURE. THE LAST NUMERIC COLUMN REPRESENTS THE RMS OF THE 35 INDIVIDUAL SIMULATED ANNEALING STRUCTURES FOUND IN PDB ENTRY 2EZE ABOUT THE MEAN COORDINATE POSITIONS. THE LAST NUMERIC COLUMN IN THE INDIVIDUAL SA STRUCTURES HAS NO MEANING. RESIDUES 3 - 27 OF THE PROTEIN CORRESPOND TO RESIDUES 51 - 75 OF INTACT HMG-I(Y). RESIDUES 3 - 5 AND 20 - 27 ARE DISORDERED. ONLY RESIDUES 3 - 23 ARE PROVIDED FOR THE RESTRAINED REGULARIZED MEAN STRUCTURE. simulated annealing BRUNGER refinement X-PLOR 3.1 structure solution XPLOR MODIFIED MODIFIED 600 Bruker AMX500 500 Bruker AMX600 750 Bruker DMX600 750 Bruker DMX750 G 201 n 1 DG 201 B G 202 n 2 DG 202 B G 203 n 3 DG 203 B A 204 n 4 DA 204 B A 205 n 5 DA 205 B A 206 n 6 DA 206 B T 207 n 7 DT 207 B T 208 n 8 DT 208 B C 209 n 9 DC 209 B C 210 n 10 DC 210 B T 211 n 11 DT 211 B C 212 n 12 DC 212 B G 213 n 1 DG 213 C A 214 n 2 DA 214 C G 215 n 3 DG 215 C G 216 n 4 DG 216 C A 217 n 5 DA 217 C A 218 n 6 DA 218 C T 219 n 7 DT 219 C T 220 n 8 DT 220 C T 221 n 9 DT 221 C C 222 n 10 DC 222 C C 223 n 11 DC 223 C C 224 n 12 DC 224 C VAL 3 n 1 VAL 3 A PRO 4 n 2 PRO 4 A THR 5 n 3 THR 5 A PRO 6 n 4 PRO 6 A LYS 7 n 5 LYS 7 A ARG 8 n 6 ARG 8 A PRO 9 n 7 PRO 9 A ARG 10 n 8 ARG 10 A GLY 11 n 9 GLY 11 A ARG 12 n 10 ARG 12 A PRO 13 n 11 PRO 13 A LYS 14 n 12 LYS 14 A GLY 15 n 13 GLY 15 A SER 16 n 14 SER 16 A LYS 17 n 15 LYS 17 A ASN 18 n 16 ASN 18 A LYS 19 n 17 LYS 19 A GLY 20 n 18 GLY 20 A ALA 21 n 19 ALA 21 A ALA 22 n 20 ALA 22 A LYS 23 n 21 LYS 23 A n 22 24 A n 23 25 A n 24 26 A n 25 27 A author_defined_assembly 3 trimeric 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 THR 24 C THR 22 1 Y 1 A ARG 25 C ARG 23 1 Y 1 A LYS 26 C LYS 24 1 Y 1 A THR 27 C THR 25 1 Y 1 A PRO 6 -49.94 81.01 1 A PRO 13 -42.71 153.61 model building X-PLOR 3.1 refinement X-PLOR 3.1 phasing X-PLOR 3.1 SOLUTION STRUCTURE OF A COMPLEX OF THE SECOND DNA BINDING DOMAIN OF HUMAN HMG-I(Y) BOUND TO DNA DODECAMER CONTAINING THE PRDII SITE OF THE INTERFERON-BETA PROMOTER, NMR, MINIMIZED AVERAGE STRUCTURE 1 N N 2 N N 3 N N hydrog WATSON-CRICK B DG 201 A N1 DG 1 1_555 C DC 224 B N3 DC 12 1_555 hydrog WATSON-CRICK B DG 201 A N2 DG 1 1_555 C DC 224 B O2 DC 12 1_555 hydrog WATSON-CRICK B DG 201 A O6 DG 1 1_555 C DC 224 B N4 DC 12 1_555 hydrog WATSON-CRICK B DG 202 A N1 DG 2 1_555 C DC 223 B N3 DC 11 1_555 hydrog WATSON-CRICK B DG 202 A N2 DG 2 1_555 C DC 223 B O2 DC 11 1_555 hydrog WATSON-CRICK B DG 202 A O6 DG 2 1_555 C DC 223 B N4 DC 11 1_555 hydrog WATSON-CRICK B DG 203 A N1 DG 3 1_555 C DC 222 B N3 DC 10 1_555 hydrog WATSON-CRICK B DG 203 A N2 DG 3 1_555 C DC 222 B O2 DC 10 1_555 hydrog WATSON-CRICK B DG 203 A O6 DG 3 1_555 C DC 222 B N4 DC 10 1_555 hydrog WATSON-CRICK B DA 204 A N1 DA 4 1_555 C DT 221 B N3 DT 9 1_555 hydrog WATSON-CRICK B DA 204 A N6 DA 4 1_555 C DT 221 B O4 DT 9 1_555 hydrog WATSON-CRICK B DA 205 A N1 DA 5 1_555 C DT 220 B N3 DT 8 1_555 hydrog WATSON-CRICK B DA 205 A N6 DA 5 1_555 C DT 220 B O4 DT 8 1_555 hydrog WATSON-CRICK B DA 206 A N1 DA 6 1_555 C DT 219 B N3 DT 7 1_555 hydrog WATSON-CRICK B DA 206 A N6 DA 6 1_555 C DT 219 B O4 DT 7 1_555 hydrog WATSON-CRICK B DT 207 A N3 DT 7 1_555 C DA 218 B N1 DA 6 1_555 hydrog WATSON-CRICK B DT 207 A O4 DT 7 1_555 C DA 218 B N6 DA 6 1_555 hydrog WATSON-CRICK B DT 208 A N3 DT 8 1_555 C DA 217 B N1 DA 5 1_555 hydrog WATSON-CRICK B DT 208 A O4 DT 8 1_555 C DA 217 B N6 DA 5 1_555 hydrog WATSON-CRICK B DC 209 A N3 DC 9 1_555 C DG 216 B N1 DG 4 1_555 hydrog WATSON-CRICK B DC 209 A N4 DC 9 1_555 C DG 216 B O6 DG 4 1_555 hydrog WATSON-CRICK B DC 209 A O2 DC 9 1_555 C DG 216 B N2 DG 4 1_555 hydrog WATSON-CRICK B DC 210 A N3 DC 10 1_555 C DG 215 B N1 DG 3 1_555 hydrog WATSON-CRICK B DC 210 A N4 DC 10 1_555 C DG 215 B O6 DG 3 1_555 hydrog WATSON-CRICK B DC 210 A O2 DC 10 1_555 C DG 215 B N2 DG 3 1_555 hydrog WATSON-CRICK B DT 211 A N3 DT 11 1_555 C DA 214 B N1 DA 2 1_555 hydrog WATSON-CRICK B DT 211 A O4 DT 11 1_555 C DA 214 B N6 DA 2 1_555 hydrog WATSON-CRICK B DC 212 A N3 DC 12 1_555 C DG 213 B N1 DG 1 1_555 hydrog WATSON-CRICK B DC 212 A N4 DC 12 1_555 C DG 213 B O6 DG 1 1_555 hydrog WATSON-CRICK B DC 212 A O2 DC 12 1_555 C DG 213 B N2 DG 1 1_555 DNA BINDING PROTEIN/DNA DNA BINDING PROTEIN, MINOR GROOVE DNA BINDING, TRANSCRIPTIONAL CO-ACTIVATOR, ARCHITECTURAL FACTOR, COMPLEX (DNA-BINDING PROTEIN-DNA), DNA BINDING PROTEIN-DNA COMPLEX HMGIY_HUMAN UNP 3 P17096 2EZD PDB 1 2EZD 2EZD PDB 2 2EZD 39 59 2EZD 3 23 P17096 A 1 1 21 201 212 2EZD 201 212 2EZD B 2 1 12 213 224 2EZD 213 224 2EZD C 3 1 12 1 P 1