HEADER MEMBRANE PROTEIN 09-JUN-23 8PC4 TITLE MEMBRANE TARGET COMPLEX 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: N-ACYL-PHOSPHATIDYLETHANOLAMINE-HYDROLYZING PHOSPHOLIPASE COMPND 3 D; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: N-ACYL PHOSPHATIDYLETHANOLAMINE PHOSPHOLIPASE D,NAPE-PLD, COMPND 6 NAPE-HYDROLYZING PHOSPHOLIPASE D; COMPND 7 EC: 3.1.4.54; COMPND 8 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: NAPEPLD, C7ORF18; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA PHAGE ECSZW-2; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 2419741 KEYWDS MEMBRANE, TARGET, DIMER, DRUG, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.GARAU REVDAT 2 05-MAR-25 8PC4 1 JRNL REVDAT 1 26-JUN-24 8PC4 0 JRNL AUTH S.CHIARUGI,F.MARGHERITI,V.DE LORENZI,E.MARTINO, JRNL AUTH 2 E.G.MARGHERITIS,A.MOSCARDINI,R.MAROTTA,A.CHAVES-SANJUAN, JRNL AUTH 3 C.DEL SEPPIA,G.FEDERIGHI,D.LAPI,T.BANDIERA,S.RAPPOSELLI, JRNL AUTH 4 R.SCURI,M.BOLOGNESI,G.GARAU JRNL TITL NAPE-PLD IS TARGET OF THIAZIDE DIURETICS JRNL REF CELL CHEM BIOL 2025 JRNL REFN ESSN 2451-9456 JRNL DOI 10.1016/J.CHEMBIOL.2025.01.008 REMARK 2 REMARK 2 RESOLUTION. 2.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 54.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 28405 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.265 REMARK 3 FREE R VALUE : 0.301 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.170 REMARK 3 FREE R VALUE TEST SET COUNT : 1468 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 54.7500 - 6.1400 1.00 2999 168 0.2423 0.2705 REMARK 3 2 6.1300 - 4.8700 1.00 2765 160 0.2311 0.3341 REMARK 3 3 4.8700 - 4.2600 1.00 2727 141 0.2194 0.2348 REMARK 3 4 4.2600 - 3.8700 1.00 2697 151 0.2422 0.2553 REMARK 3 5 3.8700 - 3.5900 1.00 2672 136 0.2729 0.3042 REMARK 3 6 3.5900 - 3.3800 1.00 2628 144 0.3200 0.3500 REMARK 3 7 3.3800 - 3.2100 1.00 2652 137 0.3334 0.3360 REMARK 3 8 3.2100 - 3.0700 0.99 2640 131 0.3537 0.3828 REMARK 3 9 3.0700 - 2.9500 0.99 2580 146 0.4246 0.4346 REMARK 3 10 2.9500 - 2.8500 0.99 2577 154 0.4681 0.5118 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.514 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.919 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 87.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 100.5 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 6111 REMARK 3 ANGLE : 1.261 8382 REMARK 3 CHIRALITY : 0.068 892 REMARK 3 PLANARITY : 0.009 1019 REMARK 3 DIHEDRAL : 19.925 2197 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -2.9186 25.4108 187.5562 REMARK 3 T TENSOR REMARK 3 T11: 0.9212 T22: 0.4044 REMARK 3 T33: 0.5500 T12: 0.2059 REMARK 3 T13: 0.0281 T23: -0.0520 REMARK 3 L TENSOR REMARK 3 L11: 2.4491 L22: 0.9091 REMARK 3 L33: 1.9309 L12: 0.0462 REMARK 3 L13: 1.0426 L23: 0.1898 REMARK 3 S TENSOR REMARK 3 S11: 0.0183 S12: 0.0354 S13: -0.0961 REMARK 3 S21: 0.1456 S22: -0.0277 S23: 0.0214 REMARK 3 S31: -0.1481 S32: 0.1481 S33: 0.0368 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 57 through 71 or REMARK 3 resid 73 through 75 or resid 77 through REMARK 3 115 or resid 117 through 166 or resid 168 REMARK 3 through 314 or resid 316 through 370 or REMARK 3 resid 372 through 388 or resid 401 REMARK 3 through 605)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 57 through 71 or REMARK 3 resid 73 through 75 or resid 77 through REMARK 3 115 or resid 117 through 166 or resid 168 REMARK 3 through 314 or resid 316 through 370 or REMARK 3 resid 372 through 388 or resid 401 REMARK 3 through 605)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8PC4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1292131039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JUL-19 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 : ELETTRA REMARK 200 BEAMLINE : 11.2C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35073 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.660 REMARK 200 RESOLUTION RANGE LOW (A) : 88.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.20 REMARK 200 R MERGE (I) : 0.14200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.02 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.50000 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.51 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 294.88333 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 147.44167 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 221.16250 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 73.72083 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 368.60417 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 294.88333 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 147.44167 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 73.72083 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 221.16250 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 368.60417 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 GLU A 3 REMARK 465 ASN A 4 REMARK 465 GLU A 5 REMARK 465 SER A 6 REMARK 465 ASN A 7 REMARK 465 GLN A 8 REMARK 465 SER A 9 REMARK 465 LEU A 10 REMARK 465 MET A 11 REMARK 465 THR A 12 REMARK 465 SER A 13 REMARK 465 SER A 14 REMARK 465 GLN A 15 REMARK 465 TYR A 16 REMARK 465 PRO A 17 REMARK 465 LYS A 18 REMARK 465 GLU A 19 REMARK 465 ALA A 20 REMARK 465 VAL A 21 REMARK 465 ARG A 22 REMARK 465 LYS A 23 REMARK 465 ARG A 24 REMARK 465 GLN A 25 REMARK 465 ASN A 26 REMARK 465 SER A 27 REMARK 465 ALA A 28 REMARK 465 ARG A 29 REMARK 465 ASN A 30 REMARK 465 SER A 31 REMARK 465 GLY A 32 REMARK 465 ALA A 33 REMARK 465 SER A 34 REMARK 465 ASP A 35 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 ARG A 38 REMARK 465 PHE A 39 REMARK 465 SER A 40 REMARK 465 ARG A 41 REMARK 465 LYS A 42 REMARK 465 SER A 43 REMARK 465 PHE A 44 REMARK 465 LYS A 45 REMARK 465 LEU A 46 REMARK 465 ASP A 47 REMARK 465 TYR A 48 REMARK 465 ARG A 49 REMARK 465 LEU A 50 REMARK 465 GLU A 51 REMARK 465 GLU A 52 REMARK 465 ASP A 53 REMARK 465 VAL A 54 REMARK 465 THR A 55 REMARK 465 LYS A 56 REMARK 465 ASP A 389 REMARK 465 ASP A 390 REMARK 465 GLU A 391 REMARK 465 ASN A 392 REMARK 465 PHE A 393 REMARK 465 MET B 1 REMARK 465 ASP B 2 REMARK 465 GLU B 3 REMARK 465 ASN B 4 REMARK 465 GLU B 5 REMARK 465 SER B 6 REMARK 465 ASN B 7 REMARK 465 GLN B 8 REMARK 465 SER B 9 REMARK 465 LEU B 10 REMARK 465 MET B 11 REMARK 465 THR B 12 REMARK 465 SER B 13 REMARK 465 SER B 14 REMARK 465 GLN B 15 REMARK 465 TYR B 16 REMARK 465 PRO B 17 REMARK 465 LYS B 18 REMARK 465 GLU B 19 REMARK 465 ALA B 20 REMARK 465 VAL B 21 REMARK 465 ARG B 22 REMARK 465 LYS B 23 REMARK 465 ARG B 24 REMARK 465 GLN B 25 REMARK 465 ASN B 26 REMARK 465 SER B 27 REMARK 465 ALA B 28 REMARK 465 ARG B 29 REMARK 465 ASN B 30 REMARK 465 SER B 31 REMARK 465 GLY B 32 REMARK 465 ALA B 33 REMARK 465 SER B 34 REMARK 465 ASP B 35 REMARK 465 SER B 36 REMARK 465 SER B 37 REMARK 465 ARG B 38 REMARK 465 PHE B 39 REMARK 465 SER B 40 REMARK 465 ARG B 41 REMARK 465 LYS B 42 REMARK 465 SER B 43 REMARK 465 PHE B 44 REMARK 465 LYS B 45 REMARK 465 LEU B 46 REMARK 465 ASP B 47 REMARK 465 TYR B 48 REMARK 465 ARG B 49 REMARK 465 LEU B 50 REMARK 465 GLU B 51 REMARK 465 GLU B 52 REMARK 465 ASP B 53 REMARK 465 VAL B 54 REMARK 465 THR B 55 REMARK 465 ASP B 390 REMARK 465 GLU B 391 REMARK 465 ASN B 392 REMARK 465 PHE B 393 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 LYS B 56 CG CD CE NZ 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 58 -157.59 40.39 REMARK 500 LYS A 59 122.22 68.83 REMARK 500 PHE A 65 177.11 -57.76 REMARK 500 ASN A 67 -74.30 -85.93 REMARK 500 TRP A 72 9.33 59.87 REMARK 500 TRP A 72 10.92 58.51 REMARK 500 PRO A 78 -130.84 -112.42 REMARK 500 ASN A 79 80.76 31.41 REMARK 500 LEU A 81 114.43 -27.29 REMARK 500 LEU A 84 -40.30 -130.71 REMARK 500 SER A 91 8.14 -57.11 REMARK 500 VAL A 93 72.10 47.16 REMARK 500 SER A 96 79.09 59.00 REMARK 500 PHE A 111 5.52 -67.24 REMARK 500 ALA A 118 19.71 48.88 REMARK 500 VAL A 120 -131.32 32.01 REMARK 500 GLU A 122 -115.86 -124.64 REMARK 500 HIS A 132 -117.70 34.47 REMARK 500 ASP A 140 56.01 38.09 REMARK 500 ASP A 147 61.58 38.00 REMARK 500 TRP A 233 8.68 80.65 REMARK 500 ASN A 236 -178.18 -170.79 REMARK 500 HIS A 253 -159.40 -148.71 REMARK 500 PRO A 289 -160.96 -73.95 REMARK 500 ALA A 290 -25.27 77.41 REMARK 500 LYS A 296 -71.16 -92.28 REMARK 500 ALA A 310 60.74 64.23 REMARK 500 TRP A 315 -24.42 -36.02 REMARK 500 TRP A 315 -24.38 -36.04 REMARK 500 ALA A 341 105.85 76.18 REMARK 500 HIS A 343 -171.21 58.77 REMARK 500 TRP A 344 151.61 64.11 REMARK 500 ASN A 387 55.49 -97.08 REMARK 500 SER B 57 -28.81 -168.79 REMARK 500 LYS B 58 40.65 -73.11 REMARK 500 VAL B 66 -65.18 -18.79 REMARK 500 ASN B 79 111.61 -161.55 REMARK 500 ARG B 82 168.26 59.62 REMARK 500 ILE B 85 -3.47 163.39 REMARK 500 ASP B 89 -134.65 31.38 REMARK 500 SER B 95 -145.77 -76.32 REMARK 500 PHE B 111 1.28 -68.30 REMARK 500 GLU B 122 -133.95 53.94 REMARK 500 ALA B 123 -103.79 45.55 REMARK 500 HIS B 132 -121.00 40.03 REMARK 500 ASP B 140 54.89 39.82 REMARK 500 ASP B 147 68.14 38.78 REMARK 500 ALA B 154 79.48 -101.44 REMARK 500 ASN B 263 25.55 49.86 REMARK 500 GLU B 312 -154.29 -73.40 REMARK 500 REMARK 500 THIS ENTRY HAS 53 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 3PE A 403 REMARK 610 3PE B 605 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 A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 185 NE2 REMARK 620 2 HIS A 187 ND1 76.8 REMARK 620 3 HIS A 253 NE2 85.2 79.1 REMARK 620 4 ASP A 284 OD2 87.4 163.4 94.7 REMARK 620 5 3PE A 403 O12 157.9 85.6 78.3 108.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 402 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 189 OD2 REMARK 620 2 HIS A 190 NE2 77.3 REMARK 620 3 ASP A 284 OD2 151.4 74.3 REMARK 620 4 HIS A 343 NE2 87.2 100.5 94.5 REMARK 620 5 3PE A 403 O14 104.3 158.9 103.5 100.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 603 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 185 NE2 REMARK 620 2 HIS B 187 ND1 76.1 REMARK 620 3 HIS B 253 NE2 87.3 86.5 REMARK 620 4 ASP B 284 OD2 83.3 159.3 94.4 REMARK 620 5 3PE B 605 O12 166.7 96.6 81.1 103.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 604 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 189 OD2 REMARK 620 2 HIS B 190 NE2 80.1 REMARK 620 3 ASP B 284 OD2 144.5 73.0 REMARK 620 4 HIS B 343 NE2 112.9 91.6 90.9 REMARK 620 5 3PE B 605 O14 91.4 162.8 107.7 105.5 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8PC4 RELATED DB: PDB DBREF 8PC4 A 1 393 UNP Q6IQ20 NAPEP_HUMAN 1 393 DBREF 8PC4 B 1 393 UNP Q6IQ20 NAPEP_HUMAN 1 393 SEQRES 1 A 393 MET ASP GLU ASN GLU SER ASN GLN SER LEU MET THR SER SEQRES 2 A 393 SER GLN TYR PRO LYS GLU ALA VAL ARG LYS ARG GLN ASN SEQRES 3 A 393 SER ALA ARG ASN SER GLY ALA SER ASP SER SER ARG PHE SEQRES 4 A 393 SER ARG LYS SER PHE LYS LEU ASP TYR ARG LEU GLU GLU SEQRES 5 A 393 ASP VAL THR LYS SER LYS LYS GLY LYS ASP GLY ARG PHE SEQRES 6 A 393 VAL ASN PRO TRP PRO THR TRP LYS ASN PRO SER ILE PRO SEQRES 7 A 393 ASN VAL LEU ARG TRP LEU ILE MET GLU LYS ASP HIS SER SEQRES 8 A 393 SER VAL PRO SER SER LYS GLU GLU LEU ASP LYS GLU LEU SEQRES 9 A 393 PRO VAL LEU LYS PRO TYR PHE ILE THR ASN PRO GLU GLU SEQRES 10 A 393 ALA GLY VAL ARG GLU ALA GLY LEU ARG VAL THR TRP LEU SEQRES 11 A 393 GLY HIS ALA THR VAL MET VAL GLU MET ASP GLU LEU ILE SEQRES 12 A 393 PHE LEU THR ASP PRO ILE PHE SER SER ARG ALA SER PRO SEQRES 13 A 393 SER GLN TYR MET GLY PRO LYS ARG PHE ARG ARG SER PRO SEQRES 14 A 393 CYS THR ILE SER GLU LEU PRO PRO ILE ASP ALA VAL LEU SEQRES 15 A 393 ILE SER HIS ASN HIS TYR ASP HIS LEU ASP TYR ASN SER SEQRES 16 A 393 VAL ILE ALA LEU ASN GLU ARG PHE GLY ASN GLU LEU ARG SEQRES 17 A 393 TRP PHE VAL PRO LEU GLY LEU LEU ASP TRP MET GLN LYS SEQRES 18 A 393 CYS GLY CYS GLU ASN VAL ILE GLU LEU ASP TRP TRP GLU SEQRES 19 A 393 GLU ASN CYS VAL PRO GLY HIS ASP LYS VAL THR PHE VAL SEQRES 20 A 393 PHE THR PRO SER GLN HIS TRP CYS LYS ARG THR LEU MET SEQRES 21 A 393 ASP ASP ASN LYS VAL LEU TRP GLY SER TRP SER VAL LEU SEQRES 22 A 393 GLY PRO TRP ASN ARG PHE PHE PHE ALA GLY ASP THR GLY SEQRES 23 A 393 TYR CYS PRO ALA PHE GLU GLU ILE GLY LYS ARG PHE GLY SEQRES 24 A 393 PRO PHE ASP LEU ALA ALA ILE PRO ILE GLY ALA TYR GLU SEQRES 25 A 393 PRO ARG TRP PHE MET LYS TYR GLN HIS VAL ASP PRO GLU SEQRES 26 A 393 GLU ALA VAL ARG ILE HIS THR ASP VAL GLN THR LYS LYS SEQRES 27 A 393 SER MET ALA ILE HIS TRP GLY THR PHE ALA LEU ALA ASN SEQRES 28 A 393 GLU HIS TYR LEU GLU PRO PRO VAL LYS LEU ASN GLU ALA SEQRES 29 A 393 LEU GLU ARG TYR GLY LEU ASN ALA GLU ASP PHE PHE VAL SEQRES 30 A 393 LEU LYS HIS GLY GLU SER ARG TYR LEU ASN ASN ASP ASP SEQRES 31 A 393 GLU ASN PHE SEQRES 1 B 393 MET ASP GLU ASN GLU SER ASN GLN SER LEU MET THR SER SEQRES 2 B 393 SER GLN TYR PRO LYS GLU ALA VAL ARG LYS ARG GLN ASN SEQRES 3 B 393 SER ALA ARG ASN SER GLY ALA SER ASP SER SER ARG PHE SEQRES 4 B 393 SER ARG LYS SER PHE LYS LEU ASP TYR ARG LEU GLU GLU SEQRES 5 B 393 ASP VAL THR LYS SER LYS LYS GLY LYS ASP GLY ARG PHE SEQRES 6 B 393 VAL ASN PRO TRP PRO THR TRP LYS ASN PRO SER ILE PRO SEQRES 7 B 393 ASN VAL LEU ARG TRP LEU ILE MET GLU LYS ASP HIS SER SEQRES 8 B 393 SER VAL PRO SER SER LYS GLU GLU LEU ASP LYS GLU LEU SEQRES 9 B 393 PRO VAL LEU LYS PRO TYR PHE ILE THR ASN PRO GLU GLU SEQRES 10 B 393 ALA GLY VAL ARG GLU ALA GLY LEU ARG VAL THR TRP LEU SEQRES 11 B 393 GLY HIS ALA THR VAL MET VAL GLU MET ASP GLU LEU ILE SEQRES 12 B 393 PHE LEU THR ASP PRO ILE PHE SER SER ARG ALA SER PRO SEQRES 13 B 393 SER GLN TYR MET GLY PRO LYS ARG PHE ARG ARG SER PRO SEQRES 14 B 393 CYS THR ILE SER GLU LEU PRO PRO ILE ASP ALA VAL LEU SEQRES 15 B 393 ILE SER HIS ASN HIS TYR ASP HIS LEU ASP TYR ASN SER SEQRES 16 B 393 VAL ILE ALA LEU ASN GLU ARG PHE GLY ASN GLU LEU ARG SEQRES 17 B 393 TRP PHE VAL PRO LEU GLY LEU LEU ASP TRP MET GLN LYS SEQRES 18 B 393 CYS GLY CYS GLU ASN VAL ILE GLU LEU ASP TRP TRP GLU SEQRES 19 B 393 GLU ASN CYS VAL PRO GLY HIS ASP LYS VAL THR PHE VAL SEQRES 20 B 393 PHE THR PRO SER GLN HIS TRP CYS LYS ARG THR LEU MET SEQRES 21 B 393 ASP ASP ASN LYS VAL LEU TRP GLY SER TRP SER VAL LEU SEQRES 22 B 393 GLY PRO TRP ASN ARG PHE PHE PHE ALA GLY ASP THR GLY SEQRES 23 B 393 TYR CYS PRO ALA PHE GLU GLU ILE GLY LYS ARG PHE GLY SEQRES 24 B 393 PRO PHE ASP LEU ALA ALA ILE PRO ILE GLY ALA TYR GLU SEQRES 25 B 393 PRO ARG TRP PHE MET LYS TYR GLN HIS VAL ASP PRO GLU SEQRES 26 B 393 GLU ALA VAL ARG ILE HIS THR ASP VAL GLN THR LYS LYS SEQRES 27 B 393 SER MET ALA ILE HIS TRP GLY THR PHE ALA LEU ALA ASN SEQRES 28 B 393 GLU HIS TYR LEU GLU PRO PRO VAL LYS LEU ASN GLU ALA SEQRES 29 B 393 LEU GLU ARG TYR GLY LEU ASN ALA GLU ASP PHE PHE VAL SEQRES 30 B 393 LEU LYS HIS GLY GLU SER ARG TYR LEU ASN ASN ASP ASP SEQRES 31 B 393 GLU ASN PHE HET ZN A 401 1 HET ZN A 402 1 HET 3PE A 403 44 HET DXC A 404 28 HET DXC A 405 28 HET DXC A 406 28 HET DXC A 407 28 HET DXC A 408 28 HET DXC A 409 28 HET DXC B 601 28 HET DXC B 602 28 HET ZN B 603 1 HET ZN B 604 1 HET 3PE B 605 44 HET DXC B 606 28 HET DXC B 607 28 HET HCZ B 608 17 HETNAM ZN ZINC ION HETNAM 3PE 1,2-DISTEAROYL-SN-GLYCEROPHOSPHOETHANOLAMINE HETNAM DXC (3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID HETNAM HCZ 6-CHLORO-3,4-DIHYDRO-2H-1,2,4-BENZOTHIADIAZINE-7- HETNAM 2 HCZ SULFONAMIDE 1,1-DIOXIDE HETSYN 3PE 3-SN-PHOSPHATIDYLETHANOLAMINE; 1,2-DIACYL-SN-GLYCERO-3- HETSYN 2 3PE PHOSPHOETHANOLAMINE HETSYN DXC DEOXYCHOLIC ACID FORMUL 3 ZN 4(ZN 2+) FORMUL 5 3PE 2(C41 H82 N O8 P) FORMUL 6 DXC 10(C24 H40 O4) FORMUL 19 HCZ C7 H8 CL N3 O4 S2 FORMUL 20 HOH *38(H2 O) HELIX 1 AA1 SER A 96 LEU A 104 1 9 HELIX 2 AA2 PRO A 109 ASN A 114 1 6 HELIX 3 AA3 ASP A 192 PHE A 203 1 12 HELIX 4 AA4 LEU A 215 GLY A 223 1 9 HELIX 5 AA5 ALA A 290 PHE A 298 1 9 HELIX 6 AA6 PRO A 313 LYS A 318 1 6 HELIX 7 AA7 ASP A 323 VAL A 334 1 12 HELIX 8 AA8 LEU A 355 TYR A 368 1 14 HELIX 9 AA9 SER B 96 LEU B 104 1 9 HELIX 10 AB1 PRO B 109 ASN B 114 1 6 HELIX 11 AB2 ASP B 192 PHE B 203 1 12 HELIX 12 AB3 LEU B 215 GLY B 223 1 9 HELIX 13 AB4 PRO B 289 PHE B 298 1 10 HELIX 14 AB5 PRO B 313 LYS B 318 1 6 HELIX 15 AB6 ASP B 323 VAL B 334 1 12 HELIX 16 AB7 LEU B 355 TYR B 368 1 14 SHEET 1 AA1 7 VAL A 227 LEU A 230 0 SHEET 2 AA1 7 ARG A 208 PRO A 212 1 N VAL A 211 O ILE A 228 SHEET 3 AA1 7 ALA A 180 LEU A 182 1 N VAL A 181 O PHE A 210 SHEET 4 AA1 7 LEU A 142 THR A 146 1 N LEU A 145 O ALA A 180 SHEET 5 AA1 7 VAL A 135 MET A 139 -1 N MET A 139 O LEU A 142 SHEET 6 AA1 7 LEU A 125 TRP A 129 -1 N ARG A 126 O GLU A 138 SHEET 7 AA1 7 SER A 383 LEU A 386 -1 O ARG A 384 N VAL A 127 SHEET 1 AA2 6 GLU A 234 ASN A 236 0 SHEET 2 AA2 6 THR A 245 THR A 249 -1 O PHE A 246 N ASN A 236 SHEET 3 AA2 6 SER A 269 LEU A 273 -1 O SER A 269 N THR A 249 SHEET 4 AA2 6 ARG A 278 PHE A 281 -1 O PHE A 279 N VAL A 272 SHEET 5 AA2 6 PHE A 301 ALA A 305 1 O ASP A 302 N ARG A 278 SHEET 6 AA2 6 THR A 336 SER A 339 1 O LYS A 338 N ASP A 302 SHEET 1 AA3 7 VAL B 227 LEU B 230 0 SHEET 2 AA3 7 ARG B 208 PRO B 212 1 N VAL B 211 O ILE B 228 SHEET 3 AA3 7 ALA B 180 LEU B 182 1 N VAL B 181 O PHE B 210 SHEET 4 AA3 7 LEU B 142 THR B 146 1 N LEU B 145 O LEU B 182 SHEET 5 AA3 7 VAL B 135 MET B 139 -1 N VAL B 137 O PHE B 144 SHEET 6 AA3 7 LEU B 125 TRP B 129 -1 N ARG B 126 O GLU B 138 SHEET 7 AA3 7 SER B 383 LEU B 386 -1 O ARG B 384 N VAL B 127 SHEET 1 AA4 7 GLU B 234 ASN B 236 0 SHEET 2 AA4 7 THR B 245 THR B 249 -1 O PHE B 246 N ASN B 236 SHEET 3 AA4 7 SER B 269 LEU B 273 -1 O SER B 269 N THR B 249 SHEET 4 AA4 7 ARG B 278 PHE B 281 -1 O PHE B 281 N TRP B 270 SHEET 5 AA4 7 PHE B 301 PRO B 307 1 O ASP B 302 N ARG B 278 SHEET 6 AA4 7 THR B 336 ILE B 342 1 O LYS B 337 N PHE B 301 SHEET 7 AA4 7 PHE B 375 PHE B 376 1 O PHE B 376 N SER B 339 LINK NE2 HIS A 185 ZN ZN A 401 1555 1555 2.29 LINK ND1 HIS A 187 ZN ZN A 401 1555 1555 2.29 LINK OD2 ASP A 189 ZN ZN A 402 1555 1555 2.06 LINK NE2 HIS A 190 ZN ZN A 402 1555 1555 2.25 LINK NE2 HIS A 253 ZN ZN A 401 1555 1555 2.29 LINK OD2 ASP A 284 ZN ZN A 401 1555 1555 2.34 LINK OD2 ASP A 284 ZN ZN A 402 1555 1555 2.07 LINK NE2 HIS A 343 ZN ZN A 402 1555 1555 2.35 LINK ZN ZN A 401 O12 3PE A 403 1555 1555 2.05 LINK ZN ZN A 402 O14 3PE A 403 1555 1555 2.24 LINK NE2 HIS B 185 ZN ZN B 603 1555 1555 2.26 LINK ND1 HIS B 187 ZN ZN B 603 1555 1555 2.27 LINK OD2 ASP B 189 ZN ZN B 604 1555 1555 2.16 LINK NE2 HIS B 190 ZN ZN B 604 1555 1555 2.30 LINK NE2 HIS B 253 ZN ZN B 603 1555 1555 2.31 LINK OD2 ASP B 284 ZN ZN B 603 1555 1555 2.54 LINK OD2 ASP B 284 ZN ZN B 604 1555 1555 2.10 LINK NE2 HIS B 343 ZN ZN B 604 1555 1555 2.33 LINK ZN ZN B 603 O12 3PE B 605 1555 1555 1.97 LINK ZN ZN B 604 O14 3PE B 605 1555 1555 1.91 CISPEP 1 GLY A 299 PRO A 300 0 7.59 CISPEP 2 GLU A 312 PRO A 313 0 -29.73 CISPEP 3 ASP B 62 GLY B 63 0 9.37 CRYST1 94.389 94.389 442.325 90.00 90.00 120.00 P 65 2 2 24 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 0.010594 0.006117 0.000000 0.00000 SCALE2 0.000000 0.012233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.002261 0.00000 MTRIX1 1 -0.457594 -0.877943 -0.140797 44.49914 1 MTRIX2 1 -0.877980 0.421107 0.227641 -30.25002 1 MTRIX3 1 -0.140565 0.227784 -0.963512 362.03422 1