PDB Short entry for 1R1I HEADER HYDROLASE 24-SEP-03 1R1I TITLE STRUCTURAL ANALYSIS OF NEPRILYSIN WITH VARIOUS SPECIFIC AND POTENT TITLE 2 INHIBITORS CAVEAT 1R1I TI1 A 2001 HAS WRONG CHIRALITY AT ATOM CA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEPRILYSIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EXTRACELLULAR DOMAIN (RESIDUE 54-749); COMPND 5 SYNONYM: NEUTRAL ENDOPEPTIDASE, NEP, ENKEPHALINASE, COMMON ACUTE COMPND 6 LYMPHOCYTIC LEUKEMIA ANTIGEN, CALLA, NEUTRAL ENDOPEPTIDASE 24.11, COMPND 7 CD10; COMPND 8 EC: 3.4.24.11; 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: MME OR EPN; SOURCE 6 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 7 EXPRESSION_SYSTEM_COMMON: BAKER'S YEAST; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: YEAST; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PPICZ-ALPHA KEYWDS LT1_9, GLYCOPROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.OEFNER,B.P.ROQUES,M.C.FOURNIE-ZALUSKI,G.E.DALE REVDAT 4 29-JUL-20 1R1I 1 CAVEAT COMPND REMARK HETNAM REVDAT 4 2 1 LINK SITE REVDAT 3 13-JUL-11 1R1I 1 VERSN REVDAT 2 24-FEB-09 1R1I 1 VERSN REVDAT 1 28-SEP-04 1R1I 0 JRNL AUTH C.OEFNER,B.P.ROQUES,M.C.FOURNIE-ZALUSKI,G.E.DALE JRNL TITL STRUCTURAL ANALYSIS OF NEPRILYSIN WITH VARIOUS SPECIFIC AND JRNL TITL 2 POTENT INHIBITORS. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 60 392 2004 JRNL REFN ISSN 0907-4449 JRNL PMID 14747736 JRNL DOI 10.1107/S0907444903027410 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.0 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) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 22350 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) : 0.280 REMARK 3 R VALUE (WORKING SET) : 0.276 REMARK 3 FREE R VALUE : 0.358 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1186 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3237 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3800 REMARK 3 BIN FREE R VALUE SET COUNT : 154 REMARK 3 BIN FREE R VALUE : 0.4880 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5595 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 19 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.36 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.12000 REMARK 3 B22 (A**2) : 2.12000 REMARK 3 B33 (A**2) : -3.17000 REMARK 3 B12 (A**2) : 1.06000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.482 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.621 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 29.403 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.906 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.840 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5790 ; 0.013 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 5073 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7836 ; 1.491 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11845 ; 0.668 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 695 ;13.048 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 1037 ;28.730 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 842 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6441 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1160 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2217 ; 0.370 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 6428 ; 0.348 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 3 ; 0.734 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 371 ; 0.288 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): 32 ; 0.237 ; 0.500 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.250 ; 0.500 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 29 ; 0.510 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 36 ; 0.366 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 1.115 ; 0.500 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): 3461 ; 4.170 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5572 ; 6.268 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2329 ; 3.810 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2264 ; 5.761 ; 3.000 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 4 REMARK 4 1R1I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020323. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25414 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.550 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.27200 REMARK 200 R SYM FOR SHELL (I) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.38067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.69033 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.69033 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.38067 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 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 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 PRO A 742 NZ LYS A 745 1.36 REMARK 500 OD1 ASP A 484 NZ LYS A 491 1.45 REMARK 500 O ARG A 735 OG SER A 738 1.58 REMARK 500 O ARG A 467 N GLU A 470 1.72 REMARK 500 C LEU A 559 CE2 PHE A 564 1.72 REMARK 500 NZ LYS A 471 O PHE A 596 1.75 REMARK 500 OE1 GLN A 70 O HOH A 15 1.79 REMARK 500 O LEU A 559 CE2 PHE A 564 1.84 REMARK 500 O MET A 272 CG1 VAL A 275 1.85 REMARK 500 CD2 LEU A 68 CD1 LEU A 687 1.88 REMARK 500 O ILE A 718 CD1 LEU A 722 1.94 REMARK 500 O VAL A 438 OD2 ASP A 441 2.00 REMARK 500 OE1 GLU A 281 OH TYR A 361 2.00 REMARK 500 O LEU A 156 N LEU A 159 2.01 REMARK 500 OH TYR A 501 OD1 ASN A 513 2.03 REMARK 500 OG1 THR A 303 CB ALA A 305 2.04 REMARK 500 O LEU A 298 ND2 ASN A 300 2.06 REMARK 500 O VAL A 204 NE2 GLN A 521 2.06 REMARK 500 ND2 ASN A 327 O ILE A 337 2.08 REMARK 500 OE1 GLU A 314 CA PRO A 319 2.08 REMARK 500 O SER A 738 N ASN A 741 2.09 REMARK 500 O GLU A 469 CB ALA A 472 2.10 REMARK 500 O ILE A 558 N GLN A 560 2.11 REMARK 500 O LYS A 355 OG1 THR A 359 2.11 REMARK 500 CD LYS A 502 OE2 GLU A 505 2.14 REMARK 500 OD1 ASP A 530 N ASP A 532 2.14 REMARK 500 O SER A 58 N ILE A 62 2.15 REMARK 500 OD1 ASP A 590 N ASN A 592 2.15 REMARK 500 O TYR A 386 OG SER A 389 2.15 REMARK 500 O GLY A 153 CD2 LEU A 156 2.16 REMARK 500 O GLU A 184 CB ALA A 188 2.16 REMARK 500 O LEU A 156 CD2 LEU A 160 2.16 REMARK 500 NH2 ARG A 140 OE1 GLU A 503 2.17 REMARK 500 OD1 ASP A 461 OG1 THR A 607 2.19 REMARK 500 NZ LYS A 196 OD1 ASP A 377 2.19 REMARK 500 O ARG A 256 N GLU A 259 2.19 REMARK 500 OE1 GLU A 646 O1 TI1 A 2001 2.19 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 16 O HOH A 16 4556 1.18 REMARK 500 NE2 GLN A 175 C LEU A 261 6765 1.74 REMARK 500 NE2 GLN A 175 O LEU A 261 6765 1.91 REMARK 500 ND2 ASN A 490 OE1 GLN A 609 5665 2.02 REMARK 500 NE2 GLN A 175 CA LEU A 261 6765 2.08 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 111 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 207 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 ASP A 365 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 489 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 504 CB - CG - OD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 VAL A 540 CB - CA - C ANGL. DEV. = -11.7 DEGREES REMARK 500 ASP A 604 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 631 CB - CG - OD2 ANGL. DEV. = 6.3 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 ILE A 55 122.33 -25.38 REMARK 500 PRO A 78 -39.42 -37.53 REMARK 500 PRO A 124 145.66 -37.96 REMARK 500 SER A 150 -52.73 -19.16 REMARK 500 GLU A 174 -37.07 -36.84 REMARK 500 TRP A 181 131.72 -10.26 REMARK 500 ALA A 183 -78.35 7.35 REMARK 500 ALA A 186 -72.59 -53.71 REMARK 500 LEU A 199 -64.24 65.55 REMARK 500 CYS A 233 32.62 79.76 REMARK 500 ILE A 236 3.07 -67.81 REMARK 500 GLN A 257 -54.46 -29.24 REMARK 500 ALA A 269 -26.60 -29.41 REMARK 500 LEU A 270 -60.27 -94.22 REMARK 500 LEU A 304 -26.95 -30.53 REMARK 500 ALA A 305 -83.86 -53.16 REMARK 500 LYS A 318 -112.10 -79.49 REMARK 500 SER A 331 39.44 -72.07 REMARK 500 ASN A 334 52.17 27.33 REMARK 500 ASN A 339 16.08 -66.95 REMARK 500 PRO A 348 -69.55 -27.44 REMARK 500 MET A 376 -70.83 -32.51 REMARK 500 LEU A 382 -158.02 -129.11 REMARK 500 GLU A 388 -43.49 -27.99 REMARK 500 SER A 389 -14.86 -49.47 REMARK 500 MET A 418 50.96 -145.00 REMARK 500 ALA A 430 -30.75 -137.46 REMARK 500 SER A 435 -77.71 -2.39 REMARK 500 GLN A 452 -54.34 -17.77 REMARK 500 ALA A 468 -57.88 -28.82 REMARK 500 ALA A 472 -107.59 4.06 REMARK 500 ASP A 484 -65.60 -29.62 REMARK 500 ASP A 504 30.04 -97.97 REMARK 500 GLU A 505 47.04 -140.84 REMARK 500 PHE A 516 -92.71 -39.11 REMARK 500 LEU A 525 -58.45 -29.52 REMARK 500 VAL A 529 116.51 -16.25 REMARK 500 VAL A 541 68.69 -107.43 REMARK 500 LEU A 559 65.65 -64.74 REMARK 500 ASP A 590 -172.43 -69.06 REMARK 500 ASN A 592 -66.18 -93.37 REMARK 500 THR A 607 120.79 -39.59 REMARK 500 GLN A 608 -54.59 -20.08 REMARK 500 GLN A 624 -74.68 -50.11 REMARK 500 GLN A 636 147.37 -39.32 REMARK 500 LEU A 638 169.19 -41.32 REMARK 500 ASN A 663 -37.44 -31.15 REMARK 500 ILE A 665 -81.68 -27.44 REMARK 500 VAL A 692 -33.31 -39.55 REMARK 500 PHE A 728 -81.88 -66.42 REMARK 500 REMARK 500 THIS ENTRY HAS 55 RAMACHANDRAN OUTLIERS. 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 GLY A 54 ILE A 55 130.15 REMARK 500 THR A 170 GLU A 171 146.67 REMARK 500 TRP A 181 THR A 182 141.60 REMARK 500 THR A 182 ALA A 183 141.41 REMARK 500 ASN A 316 GLY A 317 -143.14 REMARK 500 GLY A 317 LYS A 318 146.48 REMARK 500 LYS A 318 PRO A 319 37.00 REMARK 500 THR A 332 VAL A 333 133.57 REMARK 500 ILE A 335 SER A 336 -149.60 REMARK 500 THR A 352 LYS A 353 -148.93 REMARK 500 SER A 389 ARG A 390 -144.82 REMARK 500 ALA A 429 ALA A 430 -126.30 REMARK 500 PHE A 431 ALA A 432 -137.32 REMARK 500 GLU A 434 SER A 435 142.36 REMARK 500 GLN A 452 THR A 453 -135.01 REMARK 500 ASP A 484 ILE A 485 -142.21 REMARK 500 SER A 487 ASN A 488 -146.19 REMARK 500 LYS A 523 LYS A 524 -140.44 REMARK 500 ALA A 538 ALA A 539 -139.44 REMARK 500 ALA A 539 VAL A 540 -146.31 REMARK 500 HIS A 587 GLY A 588 139.93 REMARK 500 HIS A 711 SER A 712 139.66 REMARK 500 ASN A 737 SER A 738 141.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 583 NE2 REMARK 620 2 HIS A 587 NE2 105.1 REMARK 620 3 GLU A 646 OE1 96.5 101.1 REMARK 620 4 GLU A 646 OE2 153.0 74.8 57.9 REMARK 620 5 TI1 A2001 SG 123.8 76.2 139.1 82.8 REMARK 620 6 TI1 A2001 O1 81.9 171.5 73.0 96.8 104.1 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1DMT RELATED DB: PDB REMARK 900 RELATED ID: 1R1H RELATED DB: PDB REMARK 900 RELATED ID: 1R1J RELATED DB: PDB DBREF 1R1I A 54 749 UNP P08473 NEP_HUMAN 54 749 SEQRES 1 A 696 GLY ILE CYS LYS SER SER ASP CYS ILE LYS SER ALA ALA SEQRES 2 A 696 ARG LEU ILE GLN ASN MET ASP ALA THR THR GLU PRO CYS SEQRES 3 A 696 THR ASP PHE PHE LYS TYR ALA CYS GLY GLY TRP LEU LYS SEQRES 4 A 696 ARG ASN VAL ILE PRO GLU THR SER SER ARG TYR GLY ASN SEQRES 5 A 696 PHE ASP ILE LEU ARG ASP GLU LEU GLU VAL VAL LEU LYS SEQRES 6 A 696 ASP VAL LEU GLN GLU PRO LYS THR GLU ASP ILE VAL ALA SEQRES 7 A 696 VAL GLN LYS ALA LYS ALA LEU TYR ARG SER CYS ILE ASN SEQRES 8 A 696 GLU SER ALA ILE ASP SER ARG GLY GLY GLU PRO LEU LEU SEQRES 9 A 696 LYS LEU LEU PRO ASP ILE TYR GLY TRP PRO VAL ALA THR SEQRES 10 A 696 GLU ASN TRP GLU GLN LYS TYR GLY ALA SER TRP THR ALA SEQRES 11 A 696 GLU LYS ALA ILE ALA GLN LEU ASN SER LYS TYR GLY LYS SEQRES 12 A 696 LYS VAL LEU ILE ASN LEU PHE VAL GLY THR ASP ASP LYS SEQRES 13 A 696 ASN SER VAL ASN HIS VAL ILE HIS ILE ASP GLN PRO ARG SEQRES 14 A 696 LEU GLY LEU PRO SER ARG ASP TYR TYR GLU CYS THR GLY SEQRES 15 A 696 ILE TYR LYS GLU ALA CYS THR ALA TYR VAL ASP PHE MET SEQRES 16 A 696 ILE SER VAL ALA ARG LEU ILE ARG GLN GLU GLU ARG LEU SEQRES 17 A 696 PRO ILE ASP GLU ASN GLN LEU ALA LEU GLU MET ASN LYS SEQRES 18 A 696 VAL MET GLU LEU GLU LYS GLU ILE ALA ASN ALA THR ALA SEQRES 19 A 696 LYS PRO GLU ASP ARG ASN ASP PRO MET LEU LEU TYR ASN SEQRES 20 A 696 LYS MET THR LEU ALA GLN ILE GLN ASN ASN PHE SER LEU SEQRES 21 A 696 GLU ILE ASN GLY LYS PRO PHE SER TRP LEU ASN PHE THR SEQRES 22 A 696 ASN GLU ILE MET SER THR VAL ASN ILE SER ILE THR ASN SEQRES 23 A 696 GLU GLU ASP VAL VAL VAL TYR ALA PRO GLU TYR LEU THR SEQRES 24 A 696 LYS LEU LYS PRO ILE LEU THR LYS TYR SER ALA ARG ASP SEQRES 25 A 696 LEU GLN ASN LEU MET SER TRP ARG PHE ILE MET ASP LEU SEQRES 26 A 696 VAL SER SER LEU SER ARG THR TYR LYS GLU SER ARG ASN SEQRES 27 A 696 ALA PHE ARG LYS ALA LEU TYR GLY THR THR SER GLU THR SEQRES 28 A 696 ALA THR TRP ARG ARG CYS ALA ASN TYR VAL ASN GLY ASN SEQRES 29 A 696 MET GLU ASN ALA VAL GLY ARG LEU TYR VAL GLU ALA ALA SEQRES 30 A 696 PHE ALA GLY GLU SER LYS HIS VAL VAL GLU ASP LEU ILE SEQRES 31 A 696 ALA GLN ILE ARG GLU VAL PHE ILE GLN THR LEU ASP ASP SEQRES 32 A 696 LEU THR TRP MET ASP ALA GLU THR LYS LYS ARG ALA GLU SEQRES 33 A 696 GLU LYS ALA LEU ALA ILE LYS GLU ARG ILE GLY TYR PRO SEQRES 34 A 696 ASP ASP ILE VAL SER ASN ASP ASN LYS LEU ASN ASN GLU SEQRES 35 A 696 TYR LEU GLU LEU ASN TYR LYS GLU ASP GLU TYR PHE GLU SEQRES 36 A 696 ASN ILE ILE GLN ASN LEU LYS PHE SER GLN SER LYS GLN SEQRES 37 A 696 LEU LYS LYS LEU ARG GLU LYS VAL ASP LYS ASP GLU TRP SEQRES 38 A 696 ILE SER GLY ALA ALA VAL VAL ASN ALA PHE TYR SER SER SEQRES 39 A 696 GLY ARG ASN GLN ILE VAL PHE PRO ALA GLY ILE LEU GLN SEQRES 40 A 696 PRO PRO PHE PHE SER ALA GLN GLN SER ASN SER LEU ASN SEQRES 41 A 696 TYR GLY GLY ILE GLY MET VAL ILE GLY HIS GLU ILE THR SEQRES 42 A 696 HIS GLY PHE ASP ASP ASN GLY ARG ASN PHE ASN LYS ASP SEQRES 43 A 696 GLY ASP LEU VAL ASP TRP TRP THR GLN GLN SER ALA SER SEQRES 44 A 696 ASN PHE LYS GLU GLN SER GLN CYS MET VAL TYR GLN TYR SEQRES 45 A 696 GLY ASN PHE SER TRP ASP LEU ALA GLY GLY GLN HIS LEU SEQRES 46 A 696 ASN GLY ILE ASN THR LEU GLY GLU ASN ILE ALA ASP ASN SEQRES 47 A 696 GLY GLY LEU GLY GLN ALA TYR ARG ALA TYR GLN ASN TYR SEQRES 48 A 696 ILE LYS LYS ASN GLY GLU GLU LYS LEU LEU PRO GLY LEU SEQRES 49 A 696 ASP LEU ASN HIS LYS GLN LEU PHE PHE LEU ASN PHE ALA SEQRES 50 A 696 GLN VAL TRP CYS GLY THR TYR ARG PRO GLU TYR ALA VAL SEQRES 51 A 696 ASN SER ILE LYS THR ASP VAL HIS SER PRO GLY ASN PHE SEQRES 52 A 696 ARG ILE ILE GLY THR LEU GLN ASN SER ALA GLU PHE SER SEQRES 53 A 696 GLU ALA PHE HIS CYS ARG LYS ASN SER TYR MET ASN PRO SEQRES 54 A 696 GLU LYS LYS CYS ARG VAL TRP MODRES 1R1I ASN A 144 ASN GLYCOSYLATION SITE MODRES 1R1I ASN A 324 ASN GLYCOSYLATION SITE MODRES 1R1I ASN A 627 ASN GLYCOSYLATION SITE HET NAG A 752 14 HET NAG A 753 14 HET NAG A 754 14 HET ZN A1001 1 HET TI1 A2001 26 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM ZN ZINC ION HETNAM TI1 [2(R,S)-2-SULFANYLHEPTANOYL]-PHE-ALA FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 5 ZN ZN 2+ FORMUL 6 TI1 C19 H28 N2 O4 S FORMUL 7 HOH *19(H2 O) HELIX 1 1 SER A 58 MET A 72 1 15 HELIX 2 2 ASP A 81 ASN A 94 1 14 HELIX 3 3 ASN A 105 GLN A 122 1 18 HELIX 4 4 ILE A 129 ASN A 144 1 16 HELIX 5 5 ASN A 144 ARG A 151 1 8 HELIX 6 6 GLY A 153 LYS A 158 1 6 HELIX 7 7 LEU A 159 TYR A 164 5 6 HELIX 8 8 TRP A 166 THR A 170 5 5 HELIX 9 9 ASN A 172 TYR A 177 1 6 HELIX 10 10 THR A 182 LYS A 193 1 12 HELIX 11 11 SER A 227 CYS A 233 5 7 HELIX 12 12 THR A 234 ILE A 236 5 3 HELIX 13 13 TYR A 237 ARG A 260 1 24 HELIX 14 14 ASP A 264 THR A 286 1 23 HELIX 15 15 PRO A 289 ASN A 293 5 5 HELIX 16 16 ASP A 294 TYR A 299 1 6 HELIX 17 17 LEU A 304 PHE A 311 1 8 HELIX 18 18 SER A 321 SER A 331 1 11 HELIX 19 19 ALA A 347 THR A 359 1 13 HELIX 20 20 SER A 362 VAL A 379 1 18 HELIX 21 21 SER A 380 LEU A 382 5 3 HELIX 22 22 SER A 383 SER A 389 1 7 HELIX 23 23 ARG A 390 GLY A 399 1 10 HELIX 24 24 ALA A 405 MET A 418 1 14 HELIX 25 25 MET A 418 PHE A 431 1 14 HELIX 26 26 GLU A 434 ASP A 455 1 22 HELIX 27 27 ASP A 461 ILE A 475 1 15 HELIX 28 28 ASP A 483 ASN A 488 1 6 HELIX 29 29 ASN A 488 LEU A 497 1 10 HELIX 30 30 GLU A 505 LYS A 523 1 19 HELIX 31 31 SER A 569 GLY A 576 1 8 HELIX 32 32 GLY A 576 GLY A 588 1 13 HELIX 33 33 ASN A 592 PHE A 596 5 5 HELIX 34 34 THR A 607 PHE A 628 1 22 HELIX 35 35 TRP A 630 GLY A 634 5 5 HELIX 36 36 THR A 643 GLY A 669 1 27 HELIX 37 37 ASN A 680 VAL A 692 1 13 HELIX 38 38 ARG A 698 ASP A 709 1 12 HELIX 39 39 PRO A 713 GLN A 723 1 11 HELIX 40 40 SER A 725 PHE A 732 1 8 SHEET 1 A 2 ARG A 102 GLY A 104 0 SHEET 2 A 2 GLY A 695 TYR A 697 -1 O THR A 696 N TYR A 103 SHEET 1 B 4 ASN A 201 THR A 206 0 SHEET 2 B 4 HIS A 214 ASP A 219 -1 O ASP A 219 N ASN A 201 SHEET 3 B 4 ASP A 342 VAL A 345 1 O VAL A 344 N ILE A 218 SHEET 4 B 4 ASN A 300 THR A 303 -1 N MET A 302 O VAL A 343 SHEET 1 C 3 LYS A 476 GLY A 480 0 SHEET 2 C 3 GLN A 551 PRO A 555 1 O ILE A 552 N LYS A 476 SHEET 3 C 3 PHE A 544 SER A 546 -1 N SER A 546 O GLN A 551 SSBOND 1 CYS A 56 CYS A 61 1555 1555 2.04 SSBOND 2 CYS A 79 CYS A 734 1555 1555 2.03 SSBOND 3 CYS A 87 CYS A 694 1555 1555 2.03 SSBOND 4 CYS A 142 CYS A 410 1555 1555 2.02 SSBOND 5 CYS A 233 CYS A 241 1555 1555 2.05 SSBOND 6 CYS A 620 CYS A 746 1555 1555 2.05 LINK ND2 ASN A 144 C1 NAG A 752 1555 1555 1.44 LINK ND2 ASN A 324 C1 NAG A 753 1555 1555 1.44 LINK ND2 ASN A 627 C1 NAG A 754 1555 1555 1.43 LINK ND2 ASN A 627 C2 NAG A 754 1555 1555 2.00 LINK NE2 HIS A 583 ZN ZN A1001 1555 1555 1.71 LINK NE2 HIS A 587 ZN ZN A1001 1555 1555 2.06 LINK OE1 GLU A 646 ZN ZN A1001 1555 1555 1.85 LINK OE2 GLU A 646 ZN ZN A1001 1555 1555 2.51 LINK ZN ZN A1001 SG TI1 A2001 1555 1555 2.10 LINK ZN ZN A1001 O1 TI1 A2001 1555 1555 1.84 CISPEP 1 PRO A 561 PRO A 562 0 7.15 CRYST1 108.845 108.845 113.071 90.00 90.00 120.00 P 32 2 1 6 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 0.009187 0.005304 0.000000 0.00000 SCALE2 0.000000 0.010609 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008844 0.00000