PDB Short entry for 1DGV HEADER BLOOD CLOTTING 25-NOV-99 1DGV TITLE HOMOLOGY-BASED MODEL OF APO CIB (CALCIUM-AND INTEGRIN-BINDING PROTEIN) COMPND MOL_ID: 1; COMPND 2 MOLECULE: APO CIB; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS HELICAL, EF-HAND, BLOOD CLOTTING EXPDTA SOLUTION NMR AUTHOR P.M.HWANG,H.J.VOGEL REVDAT 5 16-FEB-22 1DGV 1 REMARK SEQADV REVDAT 4 24-FEB-09 1DGV 1 VERSN REVDAT 3 01-APR-03 1DGV 1 JRNL REVDAT 2 30-AUG-00 1DGV 1 JRNL REVDAT 1 08-DEC-99 1DGV 0 JRNL AUTH P.M.HWANG,H.J.VOGEL JRNL TITL STRUCTURES OF THE PLATELET CALCIUM- AND INTEGRIN-BINDING JRNL TITL 2 PROTEIN AND THE ALPHAIIB-INTEGRIN CYTOPLASMIC DOMAIN SUGGEST JRNL TITL 3 A MECHANISM FOR CALCIUM-REGULATED RECOGNITION; HOMOLOGY JRNL TITL 4 MODELLING AND NMR STUDIES. JRNL REF J.MOL.RECOG. V. 13 83 2000 JRNL REFN ISSN 0952-3499 JRNL PMID 10822252 JRNL DOI 10.1002/(SICI)1099-1352(200003/04)13:2<83::AID-JMR491>3.3.CO JRNL DOI 2 ;2-1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DGV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000010078. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASP A 92 HG1 THR A 93 1.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 3 CD GLU A 3 OE2 0.109 REMARK 500 GLU A 7 CD GLU A 7 OE2 0.108 REMARK 500 GLU A 18 CD GLU A 18 OE2 0.107 REMARK 500 GLU A 28 CD GLU A 28 OE2 0.107 REMARK 500 GLU A 33 CD GLU A 33 OE2 0.105 REMARK 500 GLU A 38 CD GLU A 38 OE2 0.107 REMARK 500 GLU A 48 CD GLU A 48 OE2 0.107 REMARK 500 GLU A 55 CD GLU A 55 OE2 0.107 REMARK 500 GLU A 63 CD GLU A 63 OE2 0.109 REMARK 500 GLU A 81 CD GLU A 81 OE2 0.109 REMARK 500 GLU A 118 CD GLU A 118 OE2 0.108 REMARK 500 GLU A 130 CD GLU A 130 OE2 0.108 REMARK 500 GLU A 132 CD GLU A 132 OE2 0.108 REMARK 500 GLU A 140 CD GLU A 140 OE2 0.108 REMARK 500 GLU A 150 CD GLU A 150 OE2 0.108 REMARK 500 GLU A 151 CD GLU A 151 OE2 0.108 REMARK 500 GLU A 164 CD GLU A 164 OE2 0.108 REMARK 500 HIS A 167 CG HIS A 167 CD2 0.057 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 10 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 10 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 HIS A 23 ND1 - CE1 - NE2 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 24 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 25 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ASP A 76 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 76 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ASP A 82 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 82 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 85 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 85 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ASP A 92 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 92 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 97 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 HIS A 101 ND1 - CE1 - NE2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 105 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ASP A 108 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 108 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 110 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 110 CB - CG - OD2 ANGL. DEV. = -5.7 DEGREES REMARK 500 ASP A 111 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 111 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 112 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 ASP A 112 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 117 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ASP A 119 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 119 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 122 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 THR A 128 CA - CB - CG2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ASP A 133 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 135 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 146 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 146 CB - CG - OD2 ANGL. DEV. = -5.9 DEGREES REMARK 500 ASP A 153 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 153 CB - CG - OD2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ASP A 155 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 156 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ASP A 157 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 157 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 HIS A 167 ND1 - CE1 - NE2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ARG A 171 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 PRO A 173 O - C - N ANGL. DEV. = -9.6 DEGREES REMARK 500 ASP A 174 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LEU A 4 74.72 -103.86 REMARK 500 LEU A 5 -59.99 -148.79 REMARK 500 PHE A 13 33.98 -84.63 REMARK 500 GLN A 32 -55.91 -142.91 REMARK 500 ALA A 43 -61.10 -172.21 REMARK 500 LEU A 56 55.61 -110.04 REMARK 500 LYS A 57 -76.74 -131.51 REMARK 500 SER A 70 -68.33 -126.74 REMARK 500 THR A 71 -80.81 -96.93 REMARK 500 SER A 72 -86.83 89.07 REMARK 500 LYS A 75 -37.18 74.57 REMARK 500 SER A 77 -119.42 -138.34 REMARK 500 THR A 93 -50.38 157.69 REMARK 500 ASP A 111 -39.26 69.83 REMARK 500 ARG A 117 -37.67 -39.93 REMARK 500 ARG A 156 -53.15 97.42 REMARK 500 SER A 170 -8.51 -55.54 REMARK 500 SER A 172 -58.82 -158.03 REMARK 500 ASP A 174 -78.18 -154.77 REMARK 500 SER A 178 40.69 -98.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLN A 44 VAL A 45 38.25 REMARK 500 SER A 70 THR A 71 -74.83 REMARK 500 ASP A 92 THR A 93 -145.92 REMARK 500 THR A 128 GLY A 129 -148.67 REMARK 500 GLU A 151 SER A 152 149.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 PHE A 69 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DGU RELATED DB: PDB DBREF 1DGV A 1 183 UNP Q99828 KIP1_HUMAN 9 191 SEQADV 1DGV SER A 36 UNP Q99828 THR 44 CONFLICT SEQRES 1 A 183 SER LYS GLU LEU LEU ALA GLU TYR GLN ASP LEU THR PHE SEQRES 2 A 183 LEU THR LYS GLN GLU ILE LEU LEU ALA HIS ARG ARG PHE SEQRES 3 A 183 CYS GLU LEU LEU PRO GLN GLU GLN ARG SER VAL GLU SER SEQRES 4 A 183 SER LEU ARG ALA GLN VAL PRO PHE GLU GLN ILE LEU SER SEQRES 5 A 183 LEU PRO GLU LEU LYS ALA ASN PRO PHE LYS GLU ARG ILE SEQRES 6 A 183 CYS ARG VAL PHE SER THR SER PRO ALA LYS ASP SER LEU SEQRES 7 A 183 SER PHE GLU ASP PHE LEU ASP LEU LEU SER VAL PHE SER SEQRES 8 A 183 ASP THR ALA THR PRO ASP ILE LYS SER HIS TYR ALA PHE SEQRES 9 A 183 ARG ILE PHE ASP PHE ASP ASP ASP GLY THR LEU ASN ARG SEQRES 10 A 183 GLU ASP LEU SER ARG LEU VAL ASN CYS LEU THR GLY GLU SEQRES 11 A 183 GLY GLU ASP THR ARG LEU SER ALA SER GLU MET LYS GLN SEQRES 12 A 183 LEU ILE ASP ASN ILE LEU GLU GLU SER ASP ILE ASP ARG SEQRES 13 A 183 ASP GLY THR ILE ASN LEU SER GLU PHE GLN HIS VAL ILE SEQRES 14 A 183 SER ARG SER PRO ASP PHE ALA SER SER PHE LYS ILE VAL SEQRES 15 A 183 LEU HELIX 1 1 THR A 15 LEU A 30 1 16 HELIX 2 2 PRO A 46 LEU A 51 1 6 HELIX 3 3 PHE A 61 SER A 70 1 10 HELIX 4 4 SER A 79 SER A 91 1 13 HELIX 5 5 THR A 95 ASP A 108 1 14 HELIX 6 6 ARG A 117 THR A 128 1 12 HELIX 7 7 THR A 134 SER A 152 1 19 HELIX 8 8 ASN A 161 SER A 170 1 10 SHEET 1 A 2 LEU A 115 ASN A 116 0 SHEET 2 A 2 THR A 159 ILE A 160 -1 N ILE A 160 O LEU A 115 CISPEP 1 PRO A 173 ASP A 174 0 -9.59 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000