May. 9, 22:14:00 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 0.005 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 1.3 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 -------------------------------------------------------------------------------- 8.7 TRP A 49 N - CA - C 119.9 111.2 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 MET( A-113 ) THR( A-112 ) LEU( A-111 ) ILE( A-110 ) TYR( A-109 ) LYS( A-108 ) ILE( A-107 ) LEU( A-106 ) SER( A-105 ) ARG( A-104 ) ALA( A-103 ) GLU( A-102 ) TRP( A-101 ) ASP( A-100 ) ALA( A -99 ) ALA( A -98 ) LYS( A -97 ) ALA( A -96 ) GLN( A -95 ) GLY( A -94 ) ARG( A -93 ) PHE( A -92 ) GLU( A -91 ) GLY( A -90 ) SER( A -89 ) ALA( A -88 ) VAL( A -87 ) ASP( A -86 ) LEU( A -85 ) ALA( A -84 ) ASP( A -83 ) GLY( A -82 ) PHE( A -81 ) ILE( A -80 ) HIS( A -79 ) LEU( A -78 ) SER( A -77 ) ALA( A -76 ) GLY( A -75 ) GLU( A -74 ) GLN( A -73 ) ALA( A -72 ) GLN( A -71 ) GLU( A -70 ) THR( A -69 ) ALA( A -68 ) ALA( A -67 ) LYS( A -66 ) TRP( A -65 ) PHE( A -64 ) ARG( A -63 ) GLY( A -62 ) GLN( A -61 ) ALA( A -60 ) ASN( A -59 ) LEU( A -58 ) VAL( A -57 ) LEU( A -56 ) LEU( A -55 ) ALA( A -54 ) VAL( A -53 ) GLU( A -52 ) ALA( A -51 ) GLU( A -50 ) PRO( A -49 ) LEU( A -48 ) GLY( A -47 ) GLU( A -46 ) ASP( A -45 ) LEU( A -44 ) LYS( A -43 ) TRP( A -42 ) GLU( A -41 ) ALA( A -40 ) SER( A -39 ) ARG( A -38 ) GLY( A -37 ) GLY( A -36 ) ALA( A -35 ) ARG( A -34 ) PHE( A -33 ) PRO( A -32 ) HIS( A -31 ) LEU( A -30 ) TYR( A -29 ) ARG( A -28 ) PRO( A -27 ) LEU( A -26 ) LEU( A -25 ) VAL( A -24 ) SER( A -23 ) GLU( A -22 ) VAL( A -21 ) THR( A -20 ) ARG( A -19 ) GLU( A -18 ) ALA( A -17 ) ASP( A -16 ) LEU( A -15 ) ASP( A -14 ) LEU( A -13 ) ASP( A -12 ) ALA( A -11 ) ASP( A -10 ) GLY( A -9 ) VAL( A -8 ) PRO( A -7 ) GLN( A -6 ) LEU( A -5 ) GLY( A -4 ) ASP( A -3 ) HIS( A -2 ) LEU( A -1 ) ALA( A 0 ) LEU( A 1 ) PDB Chain_ID: A 1 15 SEQRES: MET THR LEU ILE TYR LYS ILE LEU SER ARG ALA GLU TRP ASP ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 16 30 SEQRES: ALA LYS ALA GLN GLY ARG PHE GLU GLY SER ALA VAL ASP LEU ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 31 45 SEQRES: ASP GLY PHE ILE HIS LEU SER ALA GLY GLU GLN ALA GLN GLU THR COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 46 60 SEQRES: ALA ALA LYS TRP PHE ARG GLY GLN ALA ASN LEU VAL LEU LEU ALA COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 61 75 SEQRES: VAL GLU ALA GLU PRO LEU GLY GLU ASP LEU LYS TRP GLU ALA SER COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 76 90 SEQRES: ARG GLY GLY ALA ARG PHE PRO HIS LEU TYR ARG PRO LEU LEU VAL COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 91 105 SEQRES: SER GLU VAL THR ARG GLU ALA ASP LEU ASP LEU ASP ALA ASP GLY COORDS: ... ... ... ... ... ... ... ... ... ... ... ... ... ... ... 106 120 SEQRES: VAL PRO GLN LEU GLY ASP HIS LEU ALA LEU THR LEU ILE TYR LYS COORDS: ... ... ... ... ... ... ... ... ... ... THR LEU ILE TYR LYS 2 6 121 135 SEQRES: ILE LEU SER ARG ALA GLU TRP ASP ALA ALA LYS ALA GLN GLY ARG COORDS: ILE LEU SER ARG ALA GLU TRP ASP ALA ALA LYS ALA GLN GLY ARG 7 21 136 150 SEQRES: PHE GLU GLY SER ALA VAL ASP LEU ALA ASP GLY PHE ILE HIS LEU COORDS: PHE GLU GLY SER ALA VAL ASP LEU ALA ASP GLY PHE ILE HIS LEU 22 36 151 165 SEQRES: SER ALA GLY GLU GLN ALA GLN GLU THR ALA ALA LYS TRP PHE ARG COORDS: SER ALA GLY GLU GLN ALA GLN GLU THR ALA ALA LYS TRP PHE ARG 37 51 166 180 SEQRES: GLY GLN ALA ASN LEU VAL LEU LEU ALA VAL GLU ALA GLU PRO LEU COORDS: GLY GLN ALA ASN LEU VAL LEU LEU ALA VAL GLU ALA GLU PRO LEU 52 66 181 195 SEQRES: GLY GLU ASP LEU LYS TRP GLU ALA SER ARG GLY GLY ALA ARG PHE COORDS: GLY GLU ASP LEU LYS TRP GLU ALA SER ARG GLY GLY ALA ARG PHE 67 81 196 210 SEQRES: PRO HIS LEU TYR ARG PRO LEU LEU VAL SER GLU VAL THR ARG GLU COORDS: PRO HIS LEU TYR ARG PRO LEU LEU VAL SER GLU VAL THR ARG GLU 82 96 211 225 SEQRES: ALA ASP LEU ASP LEU ASP ALA ASP GLY VAL PRO GLN LEU GLY ASP COORDS: ALA ASP LEU ASP LEU ASP ALA ASP GLY VAL PRO GLN LEU GLY ASP 97 111 226 229 SEQRES: HIS LEU ALA LEU COORDS: HIS LEU ALA LEU 112 115 ==> The following residues have missing atoms: RES MOD#C SEQ ATOMS GLU( A 64) CG CD OE1 OE2 ==> The following residues have extra atoms: RES MOD#C SEQ ATOMS LEU( A 115) O2