HEADER PROTEIN BINDING 01-NOV-22 8BI8 TITLE STRUCTURE OF A CYCLIC BETA-HAIRPIN PEPTIDE DERIVED FROM NEURONAL TITLE 2 NITRIC OXIDE SYNTHASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRIC OXIDE SYNTHASE, BRAIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CONSTITUTIVE NOS,NC-NOS,NOS TYPE I,NEURONAL NOS,N-NOS,NNOS, COMPND 5 PEPTIDYL-CYSTEINE S-NITROSYLASE NOS1,BNOS; COMPND 6 EC: 1.14.13.39; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: CYCLIC PEPTIDE SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS CYCLIC BETA-HAIRPIN, NEURONAL NITRIC OXIDASE SYNTHASE, INHIBITOR OF KEYWDS 2 THE NOS/PSD-95 INTERACTION, PEPTIDE DRUGS, STROKE TREATMENT, PROTEIN KEYWDS 3 BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.R.BALBOA,S.OSTERGAARD,K.STROMGAARD,S.KNAPP,A.C.JOERGER,STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (SGC) REVDAT 3 07-FEB-24 8BI8 1 REMARK REVDAT 2 05-JUL-23 8BI8 1 JRNL REVDAT 1 21-DEC-22 8BI8 0 JRNL AUTH J.R.BALBOA,D.J.ESSIG,S.MA,N.KARER,L.S.CLEMMENSEN, JRNL AUTH 2 S.W.PEDERSEN,A.C.JOERGER,S.KNAPP,S.OSTERGAARD,K.STROMGAARD JRNL TITL DEVELOPMENT OF A POTENT CYCLIC PEPTIDE INHIBITOR OF THE JRNL TITL 2 NNOS/PSD-95 INTERACTION. JRNL REF J.MED.CHEM. V. 66 976 2023 JRNL REFN ISSN 0022-2623 JRNL PMID 36580549 JRNL DOI 10.1021/ACS.JMEDCHEM.2C01803 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.355 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 7772 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.122 REMARK 3 FREE R VALUE TEST SET COUNT : 709 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 32.6700 - 2.7200 0.99 1516 154 0.2085 0.2128 REMARK 3 2 2.7200 - 2.1590 0.99 1453 136 0.2234 0.2651 REMARK 3 3 2.1590 - 1.8862 0.98 1378 148 0.1839 0.2469 REMARK 3 4 1.8862 - 1.7137 0.98 1386 136 0.2036 0.3007 REMARK 3 5 1.7137 - 1.5900 0.95 1330 135 0.2218 0.2960 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.072 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.02 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.07 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 : 0.005 419 REMARK 3 ANGLE : 1.004 581 REMARK 3 CHIRALITY : 0.048 72 REMARK 3 PLANARITY : 0.007 80 REMARK 3 DIHEDRAL : 19.616 238 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8BI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-SEP-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 : 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) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7791 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 46.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 25.50 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.29000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1QAV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% (W/V) PEG3350, 0.1 M BIS-TRIS, PH REMARK 280 5.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.82450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.09800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.09800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 12.91225 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.09800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.09800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 38.73675 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.09800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.09800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 12.91225 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.09800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.09800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 38.73675 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 25.82450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1211 LIES ON A SPECIAL POSITION. REMARK 375 HOH B1311 LIES ON A SPECIAL POSITION. 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 A1118 CG CD CE NZ REMARK 470 GLN B1104 CG CD OE1 NE2 REMARK 470 GLN B1124 CG CD OE1 NE2 DBREF 8BI8 A 1105 1125 UNP P29475 NOS1_HUMAN 105 125 DBREF 8BI8 B 1105 1225 UNP P29475 NOS1_HUMAN 105 125 SEQADV 8BI8 GLN A 1104 UNP P29475 LINKER SEQADV 8BI8 DPR A 1125 UNP P29475 PRO 125 ENGINEERED MUTATION SEQADV 8BI8 GLY A 1126 UNP P29475 LINKER SEQADV 8BI8 GLN B 1104 UNP P29475 LINKER SEQADV 8BI8 DPR B 1225 UNP P29475 PRO 125 ENGINEERED MUTATION SEQADV 8BI8 GLY B 1226 UNP P29475 LINKER SEQRES 1 A 23 GLN THR HIS LEU GLU THR THR PHE THR GLY ASP GLY THR SEQRES 2 A 23 PRO LYS THR ILE ARG VAL THR GLN DPR GLY SEQRES 1 B 23 GLN THR HIS LEU GLU THR THR PHE THR GLY ASP GLY THR SEQRES 2 B 23 PRO LYS THR ILE ARG VAL THR GLN DPR GLY HET DPR A1125 7 HET DPR B1225 14 HETNAM DPR D-PROLINE FORMUL 1 DPR 2(C5 H9 N O2) FORMUL 3 HOH *38(H2 O) SHEET 1 AA1 2 THR A1105 PHE A1111 0 SHEET 2 AA1 2 PRO A1117 THR A1123 -1 O VAL A1122 N HIS A1106 SHEET 1 AA2 2 THR B1105 PHE B1111 0 SHEET 2 AA2 2 PRO B1117 THR B1123 -1 O LYS B1118 N THR B1110 LINK N GLN A1104 C GLY A1126 1555 1555 1.34 LINK C AGLN A1124 N DPR A1125 1555 1555 1.34 LINK C BGLN A1124 N DPR A1125 1555 1555 1.34 LINK C DPR A1125 N GLY A1126 1555 1555 1.33 LINK N AGLN B1104 C AGLY B1226 1555 1555 1.33 LINK N BGLN B1104 C BGLY B1226 1555 1555 1.34 LINK C AGLN B1124 N ADPR B1225 1555 1555 1.35 LINK C BGLN B1124 N BDPR B1225 1555 1555 1.34 LINK C ADPR B1225 N AGLY B1226 1555 1555 1.33 LINK C BDPR B1225 N BGLY B1226 1555 1555 1.33 CRYST1 46.196 46.196 51.649 90.00 90.00 90.00 P 41 21 2 16 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 0.021647 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021647 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019361 0.00000