PDB Short entry for 2SEM HEADER SIGNALING PROTEIN/INHIBITOR 02-NOV-98 2SEM TITLE SEM5 SH3 DOMAIN COMPLEXED WITH PEPTOID INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (SEX MUSCLE ABNORMAL PROTEIN 5); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C-TERMINAL SH3; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PROTEIN (SH3 PEPTOID INHIBITOR); COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 OTHER_DETAILS: PEPTIDOMIMETIC INHIBITOR KEYWDS SH3 DOMAIN, INHIBITORS, PEPTOIDS, PROTEIN-PROTEIN RECOGNITION, KEYWDS 2 PROLINE-RICH MOTIFS, SIGNAL TRANSDUCTION, SIGNALING PROTEIN, KEYWDS 3 SIGNALING PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.T.NGUYEN,C.W.TURCK,F.E.COHEN,R.N.ZUCKERMANN,W.A.LIM REVDAT 6 30-AUG-23 2SEM 1 LINK REVDAT 5 13-JUL-11 2SEM 1 VERSN REVDAT 4 24-FEB-09 2SEM 1 VERSN REVDAT 3 01-APR-03 2SEM 1 JRNL REVDAT 2 15-DEC-99 2SEM 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 06-JAN-99 2SEM 0 JRNL AUTH J.T.NGUYEN,C.W.TURCK,F.E.COHEN,R.N.ZUCKERMANN,W.A.LIM JRNL TITL EXPLOITING THE BASIS OF PROLINE RECOGNITION BY SH3 AND WW JRNL TITL 2 DOMAINS: DESIGN OF N-SUBSTITUTED INHIBITORS. JRNL EDIT F.E.BLOOM JRNL REF SCIENCE V. 282 2088 1998 JRNL REFN ISSN 0036-8075 JRNL PMID 9851931 JRNL DOI 10.1126/SCIENCE.282.5396.2088 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 6144 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.800 REMARK 3 FREE R VALUE TEST SET COUNT : 665 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.29 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 664 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 11.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 78 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1092 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 79 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.124 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2SEM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-NOV-98. REMARK 100 THE DEPOSITION ID IS D_1000000015. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 123.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6144 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21200 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1SEM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.95000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8560 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE 1-ACETYL-L-PROLYL-L-PROLYL-L-PROLYL-L-VALYL-N-(1-METHYLETHYL) REMARK 400 GLYCYL-L-PROLYL-N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHYL- N~5~- REMARK 400 [AMINO(IMINIO)METHYL]-L-ORNITHINE IS PEPTIDE-LIKE, A MEMBER OF REMARK 400 INHIBITOR CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: 1-ACETYL-L-PROLYL-L-PROLYL-L-PROLYL-L-VALYL-N-(1- REMARK 400 METHYLETHYL)GLYCYL-L-PROLYL-N~5~-[AMINO(IMINIO)METHYL]-L- REMARK 400 ORNITHYL- N~5~-[AMINO(IMINIO)METHYL]-L-ORNITHINE REMARK 400 CHAIN: C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A 213 REMARK 465 ASN A 214 REMARK 465 GLU B 255 REMARK 465 ARG C 9 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 LYS A 186 39.42 -147.75 REMARK 500 ASN A 197 -130.69 60.42 REMARK 500 LYS B 257 112.09 42.14 REMARK 500 LYS B 286 44.79 -140.08 REMARK 500 ASN B 297 -124.14 59.15 REMARK 500 SER B 313 85.48 59.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN C OF SH3 PEPTOID REMARK 800 INHIBITOR REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR CHAIN D OF SH3 PEPTOID REMARK 800 INHIBITOR DBREF 2SEM A 155 214 UNP P29355 SEM5_CAEEL 155 214 DBREF 2SEM B 255 314 UNP P29355 SEM5_CAEEL 155 214 DBREF 2SEM C 1 9 PDB 2SEM 2SEM 1 9 DBREF 2SEM D 11 19 PDB 2SEM 2SEM 11 19 SEQRES 1 A 60 GLU THR LYS PHE VAL GLN ALA LEU PHE ASP PHE ASN PRO SEQRES 2 A 60 GLN GLU SER GLY GLU LEU ALA PHE LYS ARG GLY ASP VAL SEQRES 3 A 60 ILE THR LEU ILE ASN LYS ASP ASP PRO ASN TRP TRP GLU SEQRES 4 A 60 GLY GLN LEU ASN ASN ARG ARG GLY ILE PHE PRO SER ASN SEQRES 5 A 60 TYR VAL CYS PRO TYR ASN SER ASN SEQRES 1 B 60 GLU THR LYS PHE VAL GLN ALA LEU PHE ASP PHE ASN PRO SEQRES 2 B 60 GLN GLU SER GLY GLU LEU ALA PHE LYS ARG GLY ASP VAL SEQRES 3 B 60 ILE THR LEU ILE ASN LYS ASP ASP PRO ASN TRP TRP GLU SEQRES 4 B 60 GLY GLN LEU ASN ASN ARG ARG GLY ILE PHE PRO SER ASN SEQRES 5 B 60 TYR VAL CYS PRO TYR ASN SER ASN SEQRES 1 C 9 ACE PRO PRO PRO VAL IPG PRO ARG ARG SEQRES 1 D 9 ACE PRO PRO PRO VAL IPG PRO ARG ARG MODRES 2SEM IPG C 6 GLY N-ISOPROPYL GLYCINE MODRES 2SEM IPG D 16 GLY N-ISOPROPYL GLYCINE HET ACE C 1 3 HET IPG C 6 7 HET ACE D 11 3 HET IPG D 16 7 HETNAM ACE ACETYL GROUP HETNAM IPG N-ISOPROPYL GLYCINE FORMUL 3 ACE 2(C2 H4 O) FORMUL 3 IPG 2(C5 H11 N O2) FORMUL 5 HOH *79(H2 O) HELIX 1 1 SER A 205 TYR A 207 5 3 HELIX 2 2 SER B 305 TYR B 307 5 3 SHEET 1 A 5 ARG A 199 PRO A 204 0 SHEET 2 A 5 TRP A 191 LEU A 196 -1 O TRP A 192 N PHE A 203 SHEET 3 A 5 VAL A 180 ASN A 185 -1 N THR A 182 O GLN A 195 SHEET 4 A 5 PHE A 158 ALA A 161 -1 O VAL A 159 N ILE A 181 SHEET 5 A 5 VAL A 208 PRO A 210 -1 O CYS A 209 N GLN A 160 SHEET 1 B 5 ARG B 299 PRO B 304 0 SHEET 2 B 5 TRP B 291 LEU B 296 -1 O TRP B 292 N PHE B 303 SHEET 3 B 5 VAL B 280 ASN B 285 -1 N THR B 282 O GLN B 295 SHEET 4 B 5 PHE B 258 ALA B 261 -1 O VAL B 259 N ILE B 281 SHEET 5 B 5 VAL B 308 TYR B 311 -1 O CYS B 309 N GLN B 260 SSBOND 1 CYS A 209 CYS B 309 1555 1555 2.04 LINK C ACE C 1 N PRO C 2 1555 1555 1.34 LINK C VAL C 5 N IPG C 6 1555 1555 1.33 LINK C IPG C 6 N PRO C 7 1555 1555 1.34 LINK C ACE D 11 N PRO D 12 1555 1555 1.35 LINK C VAL D 15 N IPG D 16 1555 1555 1.34 LINK C IPG D 16 N PRO D 17 1555 1555 1.34 SITE 1 AC1 11 PHE A 163 GLN A 168 GLU A 172 ASN A 190 SITE 2 AC1 11 TRP A 191 ASN A 206 TYR A 207 HOH C 10 SITE 3 AC1 11 HOH C 11 HOH C 12 HOH C 13 SITE 1 AC2 14 PHE B 263 GLU B 269 SER B 270 GLU B 272 SITE 2 AC2 14 ASN B 290 TRP B 291 ILE B 302 ASN B 306 SITE 3 AC2 14 TYR B 307 HOH D 3 HOH D 6 HOH D 20 SITE 4 AC2 14 HOH D 26 HOH D 60 CRYST1 33.200 59.900 33.600 90.00 102.00 90.00 P 1 21 1 4 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 0.030120 0.000000 0.006402 0.00000 SCALE2 0.000000 0.016694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030427 0.00000 MTRIX1 1 0.026700 -0.988100 0.151700 28.46270 1 MTRIX2 1 -0.963400 -0.066000 -0.259900 34.09120 1 MTRIX3 1 0.266800 -0.139200 -0.953600 20.29690 1