HEADER HYDROLASE 30-OCT-20 5RXA TITLE INPP5D PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF THE TITLE 2 PHOSPHATASE AND C2 DOMAINS OF SHIP1 IN COMPLEX WITH Z2856434829 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLINOSITOL 3,4,5-TRISPHOSPHATE 5-PHOSPHATASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: INOSITOL POLYPHOSPHATE-5-PHOSPHATASE D,INOSITOL COMPND 5 POLYPHOSPHATE-5-PHOSPHATASE OF 145 KDA,SIP-145,PHOSPHATIDYLINOSITOL COMPND 6 4,5-BISPHOSPHATE 5-PHOSPHATASE,SH2 DOMAIN-CONTAINING INOSITOL 5'- COMPND 7 PHOSPHATASE 1,SHIP-1,P150SHIP,HP51CN; COMPND 8 EC: 3.1.3.86,3.1.3.56,3.1.3.36; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: INPP5D, SHIP, SHIP1; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS SGC - DIAMOND I04-1 FRAGMENT SCREENING, PANDDA, XCHEMEXPLORER, SHIP1, KEYWDS 2 ALZHEIMERS, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR W.J.BRADSHAW,J.A.NEWMAN,F.VON DELFT,C.H.ARROWSMITH,A.M.EDWARDS, AUTHOR 2 C.BOUNTRA,O.GILEADI REVDAT 2 14-FEB-24 5RXA 1 JRNL REVDAT 1 11-NOV-20 5RXA 0 JRNL AUTH W.J.BRADSHAW,E.C.KENNEDY,T.MOREIRA,L.A.SMITH,R.CHALK, JRNL AUTH 2 V.L.KATIS,J.L.P.BENESCH,P.E.BRENNAN,E.J.MURPHY,O.GILEADI JRNL TITL REGULATION OF INOSITOL 5-PHOSPHATASE ACTIVITY BY THE C2 JRNL TITL 2 DOMAIN OF SHIP1 AND SHIP2. JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 JRNL PMID 38309262 JRNL DOI 10.1016/J.STR.2024.01.005 REMARK 2 REMARK 2 RESOLUTION. 1.24 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.24 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.40 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 120156 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.187 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6342 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.24 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8794 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3000 REMARK 3 BIN FREE R VALUE SET COUNT : 470 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3700 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 442 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.25 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.38000 REMARK 3 B22 (A**2) : 0.47000 REMARK 3 B33 (A**2) : -0.09000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.053 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.053 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.042 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.997 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8242 ; 0.011 ; 0.015 REMARK 3 BOND LENGTHS OTHERS (A): 5128 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8068 ; 1.711 ; 1.674 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12162 ; 1.475 ; 1.609 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 829 ; 7.239 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 316 ;37.927 ;22.816 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1095 ;13.652 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 38 ;24.700 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 711 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7372 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1318 ; 0.003 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 3913 ; 1.219 ; 1.470 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3857 ; 1.219 ; 1.448 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3797 ; 2.204 ; 2.204 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5RXA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-OCT-20. REMARK 100 THE DEPOSITION ID IS D_1001403787. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91589 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 126590 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.240 REMARK 200 RESOLUTION RANGE LOW (A) : 79.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.24 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 1.35600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: PDB ENTRY 6XY7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 MM SODIUM NITRATE, 30 MM DIBASIC REMARK 280 SODIUM PHOSPHATE, 30 MM AMMONIUM SULFATE, 100 MM MES/IMIDAZOLE, REMARK 280 PH 6.5, 20% PEG500 MME, 10% PEG20000, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 31.27500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.74500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.71000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.74500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.27500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.71000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20240 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 9.0 KCAL/MOL 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 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 394 REMARK 465 MET A 395 REMARK 465 GLU A 396 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 397 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 HOH A 1298 O HOH A 1370 1.88 REMARK 500 NE2 GLN A 469 OG1 THR A 475 2.00 REMARK 500 O HOH A 1234 O HOH A 1413 2.01 REMARK 500 ND2 ASN A 499 O HOH A 1001 2.09 REMARK 500 ND2 ASN A 499 O HOH A 1001 2.09 REMARK 500 O HOH A 1009 O HOH A 1195 2.15 REMARK 500 O HOH A 1206 O HOH A 1380 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 1001 O HOH A 1298 4455 2.16 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 772 CD GLU A 772 OE2 0.071 REMARK 500 ASP A 811 C GLU A 812 N -0.144 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 ARG A 500 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 647 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES 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 TRP A 485 -113.31 53.91 REMARK 500 ALA A 514 -113.66 55.64 REMARK 500 ASN A 530 -123.33 44.29 REMARK 500 LEU A 648 -0.54 82.00 REMARK 500 TYR A 689 108.44 -160.93 REMARK 500 ASN A 719 -99.93 -96.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1441 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1442 DISTANCE = 6.74 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ELQ A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ELQ A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DMS A 905 DBREF 5RXA A 396 856 UNP Q92835 SHIP1_HUMAN 397 857 SEQADV 5RXA SER A 394 UNP Q92835 EXPRESSION TAG SEQADV 5RXA MET A 395 UNP Q92835 EXPRESSION TAG SEQRES 1 A 463 SER MET GLU GLN PRO GLU PRO ASP MET ILE THR ILE PHE SEQRES 2 A 463 ILE GLY THR TRP ASN MET GLY ASN ALA PRO PRO PRO LYS SEQRES 3 A 463 LYS ILE THR SER TRP PHE LEU SER LYS GLY GLN GLY LYS SEQRES 4 A 463 THR ARG ASP ASP SER ALA ASP TYR ILE PRO HIS ASP ILE SEQRES 5 A 463 TYR VAL ILE GLY THR GLN GLU ASP PRO LEU SER GLU LYS SEQRES 6 A 463 GLU TRP LEU GLU ILE LEU LYS HIS SER LEU GLN GLU ILE SEQRES 7 A 463 THR SER VAL THR PHE LYS THR VAL ALA ILE HIS THR LEU SEQRES 8 A 463 TRP ASN ILE ARG ILE VAL VAL LEU ALA LYS PRO GLU HIS SEQRES 9 A 463 GLU ASN ARG ILE SER HIS ILE CYS THR ASP ASN VAL LYS SEQRES 10 A 463 THR GLY ILE ALA ASN THR LEU GLY ASN LYS GLY ALA VAL SEQRES 11 A 463 GLY VAL SER PHE MET PHE ASN GLY THR SER LEU GLY PHE SEQRES 12 A 463 VAL ASN SER HIS LEU THR SER GLY SER GLU LYS LYS LEU SEQRES 13 A 463 ARG ARG ASN GLN ASN TYR MET ASN ILE LEU ARG PHE LEU SEQRES 14 A 463 ALA LEU GLY ASP LYS LYS LEU SER PRO PHE ASN ILE THR SEQRES 15 A 463 HIS ARG PHE THR HIS LEU PHE TRP PHE GLY ASP LEU ASN SEQRES 16 A 463 TYR ARG VAL ASP LEU PRO THR TRP GLU ALA GLU THR ILE SEQRES 17 A 463 ILE GLN LYS ILE LYS GLN GLN GLN TYR ALA ASP LEU LEU SEQRES 18 A 463 SER HIS ASP GLN LEU LEU THR GLU ARG ARG GLU GLN LYS SEQRES 19 A 463 VAL PHE LEU HIS PHE GLU GLU GLU GLU ILE THR PHE ALA SEQRES 20 A 463 PRO THR TYR ARG PHE GLU ARG LEU THR ARG ASP LYS TYR SEQRES 21 A 463 ALA TYR THR LYS GLN LYS ALA THR GLY MET LYS TYR ASN SEQRES 22 A 463 LEU PRO SER TRP CYS ASP ARG VAL LEU TRP LYS SER TYR SEQRES 23 A 463 PRO LEU VAL HIS VAL VAL CYS GLN SER TYR GLY SER THR SEQRES 24 A 463 SER ASP ILE MET THR SER ASP HIS SER PRO VAL PHE ALA SEQRES 25 A 463 THR PHE GLU ALA GLY VAL THR SER GLN PHE VAL SER LYS SEQRES 26 A 463 ASN GLY PRO GLY THR VAL ASP SER GLN GLY GLN ILE GLU SEQRES 27 A 463 PHE LEU ARG CYS TYR ALA THR LEU LYS THR LYS SER GLN SEQRES 28 A 463 THR LYS PHE TYR LEU GLU PHE HIS SER SER CYS LEU GLU SEQRES 29 A 463 SER PHE VAL LYS SER GLN GLU GLY GLU ASN GLU GLU GLY SEQRES 30 A 463 SER GLU GLY GLU LEU VAL VAL LYS PHE GLY GLU THR LEU SEQRES 31 A 463 PRO LYS LEU LYS PRO ILE ILE SER ASP PRO GLU TYR LEU SEQRES 32 A 463 LEU ASP GLN HIS ILE LEU ILE SER ILE LYS SER SER ASP SEQRES 33 A 463 SER ASP GLU SER TYR GLY GLU GLY CYS ILE ALA LEU ARG SEQRES 34 A 463 LEU GLU ALA THR GLU THR GLN LEU PRO ILE TYR THR PRO SEQRES 35 A 463 LEU THR HIS HIS GLY GLU LEU THR GLY HIS PHE GLN GLY SEQRES 36 A 463 GLU ILE LYS LEU GLN THR SER GLN HET ELQ A 901 17 HET ELQ A 902 17 HET DMS A 903 4 HET DMS A 904 4 HET DMS A 905 4 HETNAM ELQ [3,4-BIS(FLUORANYL)PHENYL]-(4-METHYLPIPERAZIN-1-YL) HETNAM 2 ELQ METHANONE HETNAM DMS DIMETHYL SULFOXIDE FORMUL 2 ELQ 2(C12 H14 F2 N2 O) FORMUL 4 DMS 3(C2 H6 O S) FORMUL 7 HOH *442(H2 O) HELIX 1 AA1 ILE A 421 LEU A 426 1 6 HELIX 2 AA2 ASP A 435 ASP A 439 5 5 HELIX 3 AA3 SER A 456 SER A 473 1 18 HELIX 4 AA4 PRO A 495 ASN A 499 5 5 HELIX 5 AA5 ILE A 513 LEU A 517 5 5 HELIX 6 AA6 LYS A 547 LEU A 562 1 16 HELIX 7 AA7 PRO A 594 TRP A 596 5 3 HELIX 8 AA8 GLU A 597 GLN A 607 1 11 HELIX 9 AA9 TYR A 610 SER A 615 1 6 HELIX 10 AB1 ASP A 617 GLU A 625 1 9 HELIX 11 AB2 GLN A 658 GLY A 662 5 5 HELIX 12 AB3 ASP A 792 LEU A 797 1 6 SHEET 1 AA1 7 GLN A 430 LYS A 432 0 SHEET 2 AA1 7 VAL A 684 SER A 691 -1 O SER A 691 N GLN A 430 SHEET 3 AA1 7 VAL A 703 GLY A 710 -1 O THR A 706 N GLN A 687 SHEET 4 AA1 7 MET A 402 ASN A 411 -1 N ILE A 407 O ALA A 705 SHEET 5 AA1 7 ILE A 445 GLN A 451 1 O GLY A 449 N GLY A 408 SHEET 6 AA1 7 ILE A 487 ALA A 493 -1 O VAL A 490 N ILE A 448 SHEET 7 AA1 7 LYS A 477 LEU A 484 -1 N LEU A 484 O ILE A 487 SHEET 1 AA2 5 ILE A 501 LYS A 510 0 SHEET 2 AA2 5 GLY A 521 PHE A 529 -1 O MET A 528 N SER A 502 SHEET 3 AA2 5 THR A 532 HIS A 540 -1 O THR A 532 N PHE A 529 SHEET 4 AA2 5 HIS A 580 ASP A 586 1 O PHE A 584 N VAL A 537 SHEET 5 AA2 5 ASP A 672 SER A 678 -1 O LEU A 675 N TRP A 583 SHEET 1 AA3 5 GLU A 766 GLU A 769 0 SHEET 2 AA3 5 LEU A 775 GLY A 780 -1 O LYS A 778 N GLU A 766 SHEET 3 AA3 5 GLN A 729 LEU A 739 -1 N ALA A 737 O VAL A 777 SHEET 4 AA3 5 GLU A 841 GLN A 853 -1 O GLN A 853 N GLN A 729 SHEET 5 AA3 5 LEU A 830 HIS A 838 -1 N LEU A 836 O THR A 843 SHEET 1 AA4 4 VAL A 760 LYS A 761 0 SHEET 2 AA4 4 PHE A 747 HIS A 752 -1 N PHE A 751 O VAL A 760 SHEET 3 AA4 4 HIS A 800 SER A 807 -1 O LYS A 806 N TYR A 748 SHEET 4 AA4 4 SER A 813 ALA A 820 -1 O TYR A 814 N ILE A 805 CISPEP 1 TYR A 643 ARG A 644 0 -8.66 CISPEP 2 GLY A 720 PRO A 721 0 -5.25 SITE 1 AC1 7 TYR A 440 ILE A 471 THR A 472 SER A 473 SITE 2 AC1 7 ARG A 624 GLU A 633 HOH A1260 SITE 1 AC2 8 LYS A 477 THR A 478 VAL A 479 GLU A 498 SITE 2 AC2 8 ILE A 501 VAL A 716 HOH A1031 HOH A1068 SITE 1 AC3 7 GLY A 531 THR A 532 THR A 579 THR A 712 SITE 2 AC3 7 ASP A 798 GLN A 799 HOH A1216 SITE 1 AC4 6 TYR A 679 SER A 753 SER A 754 HIS A 800 SITE 2 AC4 6 LEU A 802 HOH A1116 SITE 1 AC5 5 HIS A 576 HIS A 631 CYS A 818 THR A 834 SITE 2 AC5 5 HOH A1151 CRYST1 62.550 79.420 89.490 90.00 90.00 90.00 P 21 21 21 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 0.015987 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011174 0.00000