HEADER PROTEIN BINDING 01-NOV-22 8BI9 TITLE STRUCTURE OF A CYCLIC BETA-HAIRPIN PEPTIDE DERIVED FROM NEURONAL TITLE 2 NITRIC OXIDE SYNTHASE (T112W/T116E VARIANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: NITRIC OXIDE SYNTHASE, BRAIN; COMPND 3 CHAIN: B, A, C, D; 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 8BI9 1 REMARK REVDAT 2 05-JUL-23 8BI9 1 JRNL REVDAT 1 21-DEC-22 8BI9 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. 1.44 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) : 1.44 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.04 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.478 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 11974 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.152 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.654 REMARK 3 FREE R VALUE TEST SET COUNT : 677 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 24.0400 - 2.4617 0.95 2399 134 0.1602 0.1676 REMARK 3 2 2.4617 - 1.9542 0.98 2401 132 0.1591 0.1817 REMARK 3 3 1.9542 - 1.7072 0.96 2320 141 0.1233 0.1904 REMARK 3 4 1.7072 - 1.5512 0.96 2308 157 0.1407 0.2215 REMARK 3 5 1.5512 - 1.4400 0.78 1869 113 0.1403 0.2350 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) : 0.129 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.98 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 : 0.005 773 REMARK 3 ANGLE : 0.862 1067 REMARK 3 CHIRALITY : 0.070 117 REMARK 3 PLANARITY : 0.006 141 REMARK 3 DIHEDRAL : 21.522 273 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 8BI9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126070. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-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 : 11979 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.440 REMARK 200 RESOLUTION RANGE LOW (A) : 27.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.03000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.44 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.07700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 10.80 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 (%): 28.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% (V/V) TERT-BUTANOL, 0.1 M SODIUM REMARK 280 CITRATE PH 3.9, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 21.36950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 14.93600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 21.36950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 14.93600 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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: 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 350 REMARK 350 BIOMOLECULE: 2 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 D1206 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 GLU A1116 CG CD OE1 OE2 REMARK 470 GLU C1116 CG CD OE1 OE2 REMARK 470 GLN C1124 CG CD OE1 NE2 REMARK 470 LYS D1118 CD CE NZ DBREF 8BI9 B 1105 1125 UNP P29475 NOS1_HUMAN 105 125 DBREF 8BI9 A 1105 1125 UNP P29475 NOS1_HUMAN 105 125 DBREF 8BI9 C 1105 1125 UNP P29475 NOS1_HUMAN 105 125 DBREF 8BI9 D 1105 1125 UNP P29475 NOS1_HUMAN 105 125 SEQADV 8BI9 GLN B 1104 UNP P29475 LINKER SEQADV 8BI9 TRP B 1112 UNP P29475 THR 112 ENGINEERED MUTATION SEQADV 8BI9 GLU B 1116 UNP P29475 THR 116 ENGINEERED MUTATION SEQADV 8BI9 DPR B 1125 UNP P29475 PRO 125 ENGINEERED MUTATION SEQADV 8BI9 GLY B 1126 UNP P29475 LINKER SEQADV 8BI9 GLN A 1104 UNP P29475 LINKER SEQADV 8BI9 TRP A 1112 UNP P29475 THR 112 ENGINEERED MUTATION SEQADV 8BI9 GLU A 1116 UNP P29475 THR 116 ENGINEERED MUTATION SEQADV 8BI9 DPR A 1125 UNP P29475 PRO 125 ENGINEERED MUTATION SEQADV 8BI9 GLY A 1126 UNP P29475 LINKER SEQADV 8BI9 GLN C 1104 UNP P29475 LINKER SEQADV 8BI9 TRP C 1112 UNP P29475 THR 112 ENGINEERED MUTATION SEQADV 8BI9 GLU C 1116 UNP P29475 THR 116 ENGINEERED MUTATION SEQADV 8BI9 DPR C 1125 UNP P29475 PRO 125 ENGINEERED MUTATION SEQADV 8BI9 GLY C 1126 UNP P29475 LINKER SEQADV 8BI9 GLN D 1104 UNP P29475 LINKER SEQADV 8BI9 TRP D 1112 UNP P29475 THR 112 ENGINEERED MUTATION SEQADV 8BI9 GLU D 1116 UNP P29475 THR 116 ENGINEERED MUTATION SEQADV 8BI9 DPR D 1125 UNP P29475 PRO 125 ENGINEERED MUTATION SEQADV 8BI9 GLY D 1126 UNP P29475 LINKER SEQRES 1 B 23 GLN THR HIS LEU GLU THR THR PHE TRP GLY ASP GLY GLU SEQRES 2 B 23 PRO LYS THR ILE ARG VAL THR GLN DPR GLY SEQRES 1 A 23 GLN THR HIS LEU GLU THR THR PHE TRP GLY ASP GLY GLU SEQRES 2 A 23 PRO LYS THR ILE ARG VAL THR GLN DPR GLY SEQRES 1 C 23 GLN THR HIS LEU GLU THR THR PHE TRP GLY ASP GLY GLU SEQRES 2 C 23 PRO LYS THR ILE ARG VAL THR GLN DPR GLY SEQRES 1 D 23 GLN THR HIS LEU GLU THR THR PHE TRP GLY ASP GLY GLU SEQRES 2 D 23 PRO LYS THR ILE ARG VAL THR GLN DPR GLY HET DPR B1125 7 HET DPR A1125 14 HET DPR C1125 11 HET DPR D1125 7 HET TBU C1201 5 HETNAM DPR D-PROLINE HETNAM TBU TERTIARY-BUTYL ALCOHOL HETSYN TBU 2-METHYL-2-PROPANOL FORMUL 1 DPR 4(C5 H9 N O2) FORMUL 5 TBU C4 H10 O FORMUL 6 HOH *79(H2 O) SHEET 1 AA1 4 PRO B1117 THR B1123 0 SHEET 2 AA1 4 THR B1105 PHE B1111 -1 N HIS B1106 O VAL B1122 SHEET 3 AA1 4 THR C1105 THR C1110 -1 O THR C1109 N LEU B1107 SHEET 4 AA1 4 LYS C1118 THR C1123 -1 O VAL C1122 N HIS C1106 SHEET 1 AA2 4 PRO A1117 THR A1123 0 SHEET 2 AA2 4 THR A1105 PHE A1111 -1 N HIS A1106 O VAL A1122 SHEET 3 AA2 4 THR D1105 TRP D1112 -1 O LEU D1107 N THR A1109 SHEET 4 AA2 4 GLU D1116 THR D1123 -1 O VAL D1122 N HIS D1106 LINK N GLN B1104 C GLY B1126 1555 1555 1.32 LINK C GLN B1124 N DPR B1125 1555 1555 1.34 LINK C DPR B1125 N GLY B1126 1555 1555 1.33 LINK N GLN A1104 C GLY A1126 1555 1555 1.34 LINK C GLN A1124 N ADPR A1125 1555 1555 1.35 LINK C GLN A1124 N BDPR A1125 1555 1555 1.34 LINK C ADPR A1125 N GLY A1126 1555 1555 1.33 LINK C BDPR A1125 N GLY A1126 1555 1555 1.33 LINK N GLN C1104 C GLY C1126 1555 1555 1.34 LINK C GLN C1124 N DPR C1125 1555 1555 1.34 LINK C DPR C1125 N GLY C1126 1555 1555 1.32 LINK N GLN D1104 C GLY D1126 1555 1555 1.34 LINK C GLN D1124 N DPR D1125 1555 1555 1.34 LINK C DPR D1125 N GLY D1126 1555 1555 1.32 CRYST1 42.739 29.872 58.940 90.00 108.59 90.00 C 1 2 1 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 0.023398 0.000000 0.007871 0.00000 SCALE2 0.000000 0.033476 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017901 0.00000