May. 11, 03:20:06 2013 Greetings, [ Text modified to reflect that this was run under PSVS - Aneerban Bhattacharya: Dec 2005 ] The following checks were made on : ----------------------------------------- DISTANCES AND ANGLES We have checked your intra and intermolecular distances and angles with the procedures currently in place at PDB: ==> The following solvent molecules are further away than 3.5 Angstroms from macromolecule atoms which are available for hydrogen bonding in the asymmetric unit. none The coordinates for water molecules which could be translated back into the asymmetric unit are listed. If you do not indicate otherwise we will replace the solvent coordinates in the entry with the ones below: none ==> Close contacts in same asymmetric unit. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Close contacts based on crystal symmetry. Distances smaller than 2.2 Angstroms are considered as close contacts. none ==> Bond and angle checks are performed by first computing the average rms error for all bonds and angles relative to standard values for nucleotide units [L. Clowney et al., Geometric Parameters in Nucleic Acids: Nitrogenous Bases, J.Am.Chem.Soc. 1996, 118, 509-518; A. Gelbin et al., Geometric Parameters in Nucleic Acids: Sugar and Phosphate Constituents, J.Am.Chem.Soc. 1996, 118, 519-529] and amino acid units [R.A. Engh and R. Huber, Accurate Bond and Angle Parameters for X-ray protein structure refinement, Acta Crystallogr. 1991, A47, 392-400]. Any bond or angle which deviates from the dictionary values by more than six times this computed rms error is identified as an outlier. *** Covalent Bond Lengths: The RMS deviation for covalent bonds relative to the standard dictionary is 0.008 Angstroms All covalent bonds lie within a 6.0*RMSD range about the standard dictionary values. *** Covalent Angle Values: The RMS deviation for covalent angles relative to the standard dictionary is 1.6 degrees. The following table contains a list of the covalent bond angles greater than 6.0*RMSD. Deviation Residue Chain Sequence AT1 - AT2 - AT3 Bond Dictionary Name ID Number Angle Value -------------------------------------------------------------------------------- -10.6 ILE A 191 N - CA - C 100.6 111.2 TORSION ANGLES The torsion angle distributions have been checked. The postscript file of the conformation rings showing the torsion angle distributions will be sent in a separate E-mail message. CHIRALITY The chirality has been checked and there are no incorrect carbon chiral centers. Some of O1P and O2P atoms do not follow the convention defined in the standard IUBMB nomenclature (Liebecq, C. Compendium of Biochemical Nomenclature and Related Documents, 2nd ed.; Portland Press: London and Chapel Hill, 1992). If you do not indicate otherwise, we will switch the labels of O1P and O2P as shown below. OTHER IMPORTANT ISSUES ==> Please check carefully REMARKS 3 and 200 and fill in the parameters as appropriate. ==> The following residues are missing: (Note: The SEQ number starts from 1 for each chain according to SEQRES sequence record.) RES MOD#C SEQ MSE( A 6 ) GLU( A 7 ) ASP( A 8 ) PHE( A 9 ) LYS( A 10 ) LYS( A 11 ) ILE( A 12 ) VAL( A 13 ) ASN( A 14 ) ASN( A 15 ) ILE( A 16 ) ARG( A 17 ) LEU( A 18 ) LYS( A 19 ) ASP( A 20 ) THR( A 21 ) PHE( A 22 ) ASP( A 23 ) PHE( A 24 ) LYS( A 25 ) LEU( A 26 ) ALA( A 27 ) ALA( A 28 ) PHE( A 29 ) PRO( A 30 ) ASN( A 31 ) GLN( A 32 ) ASN( A 33 ) TYR( A 34 ) ASP( A 35 ) GLN( A 36 ) LEU( A 37 ) LEU( A 38 ) PRO( A 39 ) SER( A 40 ) GLN( A 41 ) ILE( A 42 ) TYR( A 43 ) LYS( A 44 ) ASN( A 45 ) TYR( A 46 ) TYR( A 47 ) GLN( A 48 ) GLY( A 49 ) ILE( A 50 ) GLU( A 51 ) ILE( A 52 ) GLN( A 53 ) GLN( A 54 ) HIS( A 55 ) LYS( A 56 ) TYR( A 57 ) GLN( A 58 ) ASN( A 59 ) GLU( A 60 ) LEU( A 61 ) ASP( A 62 ) ILE( A 63 ) LYS( A 64 ) ILE( A 65 ) ILE( A 66 ) ASN( A 67 ) PHE( A 68 ) LEU( A 69 ) TYR( A 70 ) PRO( A 71 ) ASP( A 72 ) GLY( A 73 ) ASP( A 74 ) PHE( A 75 ) GLY( A 76 ) SER( A 77 ) ALA( A 78 ) ASN( A 79 ) LYS( A 80 ) ASN( A 81 ) GLY( A 82 ) THR( A 83 ) LEU( A 84 ) LYS( A 85 ) LEU( A 86 ) SER( A 87 ) LEU( A 88 ) MSE( A 89 ) LEU( A 90 ) THR( A 91 ) ASP( A 92 ) LYS( A 93 ) LYS( A 94 ) ASN( A 95 ) ASN( A 96 ) GLN( A 97 ) VAL( A 98 ) TYR( A 99 ) TYR( A 100 ) LYS( A 101 ) LEU( A 102 ) LEU( A 103 ) GLU( A 104 ) VAL( A 105 ) SER( A 106 ) GLY( A 107 ) PHE( A 108 ) LYS( A 109 ) SER( A 110 ) ASN( A 111 ) PRO( A 112 ) TYR( A 113 ) GLY( A 114 ) VAL( A 115 ) ASP( A 116 ) GLU( A 117 ) ASN( A 118 ) GLY( A 119 ) THR( A 120 ) ILE( A 121 ) PRO( A 122 ) GLY( A 123 ) LEU( A 124 ) GLU( A 125 ) HIS( A 126 ) HIS( A 127 ) HIS( A 128 ) HIS( A 129 ) HIS( A 130 ) HIS( A 131 ) PDB Chain_ID: A 1 15 SEQRES: MSE GLU ASP PHE LYS LYS ILE VAL ASN ASN ILE ARG LEU LYS ASP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: THR PHE ASP PHE LYS LEU ALA ALA PHE PRO ASN GLN ASN TYR ASP COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: GLN LEU LEU PRO SER GLN ILE TYR LYS ASN TYR TYR GLN GLY ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: GLU ILE GLN GLN HIS LYS TYR GLN ASN GLU LEU ASP ILE LYS ILE COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: ILE ASN PHE LEU TYR PRO ASP GLY ASP PHE GLY SER ALA ASN LYS COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: ASN GLY THR LEU LYS LEU SER LEU MSE LEU THR ASP LYS LYS ASN COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: ASN GLN VAL TYR TYR LYS LEU LEU GLU VAL SER GLY PHE LYS SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: ASN PRO TYR GLY VAL ASP GLU ASN GLY THR ILE PRO GLY LEU GLU COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 121 135 SEQRES: HIS HIS HIS HIS HIS HIS MSE GLU ASP PHE LYS LYS ILE VAL ASN COORDS: ... ... ... ... ... ... MSE GLU ASP PHE LYS LYS ILE VAL ASN 132 140 136 150 SEQRES: ASN ILE ARG LEU LYS ASP THR PHE ASP PHE LYS LEU ALA ALA PHE COORDS: ASN ILE ARG LEU LYS ASP THR PHE ASP PHE LYS LEU ALA ALA PHE 141 155 151 165 SEQRES: PRO ASN GLN ASN TYR ASP GLN LEU LEU PRO SER GLN ILE TYR LYS COORDS: PRO ASN GLN ASN TYR ASP GLN LEU LEU PRO SER GLN ILE TYR LYS 156 170 166 180 SEQRES: ASN TYR TYR GLN GLY ILE GLU ILE GLN GLN HIS LYS TYR GLN ASN COORDS: ASN TYR TYR GLN GLY ILE GLU ILE GLN GLN HIS LYS TYR GLN ASN 171 185 181 195 SEQRES: GLU LEU ASP ILE LYS ILE ILE ASN PHE LEU TYR PRO ASP GLY ASP COORDS: GLU LEU ASP ILE LYS ILE ILE ASN PHE LEU TYR PRO ASP GLY ASP 186 200 196 210 SEQRES: PHE GLY SER ALA ASN LYS ASN GLY THR LEU LYS LEU SER LEU MSE COORDS: PHE GLY SER ALA ASN LYS ASN GLY THR LEU LYS LEU SER LEU MSE 201 215 211 225 SEQRES: LEU THR ASP LYS LYS ASN ASN GLN VAL TYR TYR LYS LEU LEU GLU COORDS: LEU THR ASP LYS LYS ASN ASN GLN VAL TYR TYR LYS LEU LEU GLU 216 230 226 240 SEQRES: VAL SER GLY PHE LYS SER ASN PRO TYR GLY VAL ASP GLU ASN GLY COORDS: VAL SER GLY PHE LYS SER ASN PRO TYR GLY VAL ASP GLU ASN GLY 231 245 241 246 SEQRES: THR ILE PRO GLY LEU GLU COORDS: THR ILE PRO GLY LEU GLU 246 251