PDB Short entry for 5MNW HEADER LYASE 13-DEC-16 5MNW TITLE SOLUTION STRUCTURE OF THE CINACIGUAT BOUND HUMAN BETA1 H-NOX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GCS-BETA-1,GUANYLATE CYCLASE SOLUBLE SUBUNIT BETA-3,GCS- COMPND 5 BETA-3,SOLUBLE GUANYLATE CYCLASE SMALL SUBUNIT; COMPND 6 EC: 4.6.1.2; COMPND 7 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: GUCY1B3, GUC1B3, GUCSB3, GUCY1B1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SOLUBLE GUANYLATE CYCLASE, H-NOX, CINACIGUAT, LYASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.MATZAPETAKIS,I.H.SARAIVA REVDAT 3 14-JUN-23 5MNW 1 REMARK REVDAT 2 08-MAY-19 5MNW 1 REMARK REVDAT 1 13-JUN-18 5MNW 0 JRNL AUTH M.MATZAPETAKIS,I.H.SARAIVA JRNL TITL SOLUTION STRUCTURE OF THE CINACIGUAT BOUND HUMAN BETA1 JRNL TITL 2 H-NOX. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.21 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MNW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002730. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 310 REMARK 210 PH : 6.5; 6.5 REMARK 210 IONIC STRENGTH : 110; 110 REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-99% 13C; U-99% 15N] REMARK 210 BETA1 H-NOX, 20 MM SODIUM REMARK 210 PHOSPHATE, 50 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 2D 1H-15N HSQC; REMARK 210 3D HNCO; 3D HCCH-TOCSY; 3D HNCA; 3D HN(CA)CO; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D 1H-15N NOESY; 3D 1H-13C NOESY; 3D HN(COCA)HA; REMARK 210 H[C(0)]_H[C(0)].RELAYED; H_H{[N(0)]+[C(0)]}.THROUGH-SPACE; H[C(0) REMARK 210 ]_H[C(0)].THROUGH-SPACE; H[C]_H{[C(0)]+[N(0)]}.THROUGH-SPACE; 2D REMARK 210 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE II REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4, ARIA 2.3, REMARK 210 TOPSPIN 3.2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 HZ2 LYS A 27 OD2 ASP A 32 1.57 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 7 TYR A 49 CZ TYR A 49 CE2 -0.085 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 1 ILE A 42 86.70 59.97 REMARK 500 1 ASN A 60 -6.25 78.08 REMARK 500 1 LYS A 127 -22.21 -164.76 REMARK 500 1 ILE A 157 -64.26 -97.61 REMARK 500 1 ASN A 171 -158.53 -148.13 REMARK 500 2 GLN A 36 -78.31 -129.29 REMARK 500 2 PHE A 37 69.24 61.95 REMARK 500 2 VAL A 94 -71.15 -80.26 REMARK 500 2 GLU A 126 -160.89 -160.55 REMARK 500 2 LYS A 127 73.28 -69.33 REMARK 500 2 GLN A 169 43.53 -93.48 REMARK 500 2 ASN A 171 -158.72 -105.95 REMARK 500 2 CYS A 174 -81.36 -118.23 REMARK 500 2 ASP A 175 -76.58 -152.97 REMARK 500 2 LYS A 184 43.21 -88.00 REMARK 500 2 LYS A 187 162.09 67.22 REMARK 500 2 GLU A 188 -59.67 69.32 REMARK 500 2 HIS A 189 64.74 -109.25 REMARK 500 2 HIS A 192 64.04 -118.54 REMARK 500 3 ILE A 42 118.39 67.12 REMARK 500 3 LYS A 129 -81.01 -143.17 REMARK 500 3 GLU A 138 48.83 -93.94 REMARK 500 3 GLU A 161 99.93 -69.80 REMARK 500 3 ASN A 171 -164.63 -161.36 REMARK 500 3 LYS A 184 49.93 -107.09 REMARK 500 3 GLU A 188 60.01 -116.87 REMARK 500 3 HIS A 191 97.29 68.38 REMARK 500 3 HIS A 193 -156.97 60.90 REMARK 500 4 TYR A 17 -56.57 -125.30 REMARK 500 4 GLU A 34 -76.03 -95.49 REMARK 500 4 PHE A 37 80.60 59.89 REMARK 500 4 ILE A 42 78.65 60.16 REMARK 500 4 LYS A 129 72.45 -112.38 REMARK 500 4 ARG A 170 97.68 -64.08 REMARK 500 4 ASN A 171 -163.28 -111.98 REMARK 500 4 GLU A 188 127.12 71.08 REMARK 500 4 HIS A 193 31.76 -97.88 REMARK 500 5 GLU A 34 73.76 56.38 REMARK 500 5 GLN A 36 101.04 66.48 REMARK 500 5 SER A 81 34.49 -95.90 REMARK 500 5 TYR A 83 170.59 -42.74 REMARK 500 5 ASP A 84 -29.01 -39.17 REMARK 500 5 LEU A 90 45.55 70.52 REMARK 500 5 GLU A 126 -81.51 -142.28 REMARK 500 5 LYS A 127 38.25 -151.60 REMARK 500 5 GLU A 140 -163.34 -105.21 REMARK 500 5 ILE A 157 -77.88 -66.19 REMARK 500 5 HIS A 158 33.67 -174.25 REMARK 500 5 THR A 160 151.80 177.66 REMARK 500 5 ASP A 175 -37.25 71.75 REMARK 500 REMARK 500 THIS ENTRY HAS 119 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Z90 A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34077 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF THE CINACIGUAT BOUND HUMAN BETA1 H-NOX. DBREF 5MNW A 1 188 UNP Q02153 GCYB1_HUMAN 1 188 SEQADV 5MNW HIS A 189 UNP Q02153 EXPRESSION TAG SEQADV 5MNW HIS A 190 UNP Q02153 EXPRESSION TAG SEQADV 5MNW HIS A 191 UNP Q02153 EXPRESSION TAG SEQADV 5MNW HIS A 192 UNP Q02153 EXPRESSION TAG SEQADV 5MNW HIS A 193 UNP Q02153 EXPRESSION TAG SEQADV 5MNW HIS A 194 UNP Q02153 EXPRESSION TAG SEQRES 1 A 194 MET TYR GLY PHE VAL ASN HIS ALA LEU GLU LEU LEU VAL SEQRES 2 A 194 ILE ARG ASN TYR GLY PRO GLU VAL TRP GLU ASP ILE LYS SEQRES 3 A 194 LYS GLU ALA GLN LEU ASP GLU GLU GLY GLN PHE LEU VAL SEQRES 4 A 194 ARG ILE ILE TYR ASP ASP SER LYS THR TYR ASP LEU VAL SEQRES 5 A 194 ALA ALA ALA SER LYS VAL LEU ASN LEU ASN ALA GLY GLU SEQRES 6 A 194 ILE LEU GLN MET PHE GLY LYS MET PHE PHE VAL PHE CYS SEQRES 7 A 194 GLN GLU SER GLY TYR ASP THR ILE LEU ARG VAL LEU GLY SEQRES 8 A 194 SER ASN VAL ARG GLU PHE LEU GLN ASN LEU ASP ALA LEU SEQRES 9 A 194 HIS ASP HIS LEU ALA THR ILE TYR PRO GLY MET ARG ALA SEQRES 10 A 194 PRO SER PHE ARG CYS THR ASP ALA GLU LYS GLY LYS GLY SEQRES 11 A 194 LEU ILE LEU HIS TYR TYR SER GLU ARG GLU GLY LEU GLN SEQRES 12 A 194 ASP ILE VAL ILE GLY ILE ILE LYS THR VAL ALA GLN GLN SEQRES 13 A 194 ILE HIS GLY THR GLU ILE ASP MET LYS VAL ILE GLN GLN SEQRES 14 A 194 ARG ASN GLU GLU CYS ASP HIS THR GLN PHE LEU ILE GLU SEQRES 15 A 194 GLU LYS GLU SER LYS GLU HIS HIS HIS HIS HIS HIS HET Z90 A 201 79 HETNAM Z90 4-({(4-CARBOXYBUTYL)[2-(2-{[4-(2-PHENYLETHYL) HETNAM 2 Z90 BENZYL]OXY}PHENYL)ETHYL]AMINO}METHYL)BENZOIC ACID HETSYN Z90 4-((4-CARBOXYBUTYL)(2-((4-PHENETHYLBENZOL)OXY) HETSYN 2 Z90 PHENETHYL) AMINO)METHYL(BENZOIC) ACID) FORMUL 2 Z90 C36 H39 N O5 HELIX 1 AA1 TYR A 2 TYR A 17 1 16 HELIX 2 AA2 GLY A 18 ALA A 29 1 12 HELIX 3 AA3 ASP A 44 LEU A 59 1 16 HELIX 4 AA4 ASN A 62 SER A 81 1 20 HELIX 5 AA5 ASP A 84 VAL A 89 1 6 HELIX 6 AA6 LEU A 90 SER A 92 5 3 HELIX 7 AA7 ASN A 93 ASN A 100 1 8 HELIX 8 AA8 ASN A 100 LEU A 108 1 9 HELIX 9 AA9 ARG A 139 GLY A 141 5 3 HELIX 10 AB1 LEU A 142 GLN A 156 1 15 HELIX 11 AB2 GLU A 185 GLU A 188 5 4 SHEET 1 AA1 4 PHE A 120 ASP A 124 0 SHEET 2 AA1 4 LEU A 131 TYR A 135 -1 O HIS A 134 N ARG A 121 SHEET 3 AA1 4 THR A 177 LYS A 184 -1 O THR A 177 N TYR A 135 SHEET 4 AA1 4 GLU A 161 GLN A 168 -1 N GLU A 161 O LYS A 184 SITE 1 AC1 11 MET A 1 TYR A 2 PHE A 4 VAL A 5 SITE 2 AC1 11 PHE A 97 LEU A 101 TYR A 112 ALA A 117 SITE 3 AC1 11 TYR A 135 SER A 137 ARG A 139 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000