HEADER CELL CYCLE 11-SEP-24 9GRM TITLE CDC42 IN COMPLEX WITH INHIBITORY PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CELL DIVISION CONTROL PROTEIN 42 HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: 1-184; COMPND 5 SYNONYM: G25K GTP-BINDING PROTEIN; COMPND 6 EC: 3.6.5.2; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PRO-SER-ILE-CYS-HIS-VAL-HIS-ARG-PRO-ASP-TRP-PRO-CYS-ALA- COMPND 11 TYR-ARG; COMPND 12 CHAIN: B; COMPND 13 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: CDC42; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS INHIBITOR, GTPASE, CYTOSKELETAL REGULATOR, CELL CYCLE EXPDTA SOLUTION NMR NUMMDL 24 AUTHOR H.R.MOTT,D.OWEN,N.P.MURPHY REVDAT 3 18-FEB-26 9GRM 1 JRNL REVDAT 2 11-FEB-26 9GRM 1 JRNL REVDAT 1 21-JAN-26 9GRM 0 JRNL AUTH N.P.MURPHY,G.J.N.TETLEY,J.REVELL,H.R.MOTT,D.OWEN JRNL TITL CYCLIZED PEPTIDE INHIBITORS OF THE SMALL G PROTEIN CDC42 JRNL TITL 2 MIMIC BINDING OF EFFECTOR PROTEINS. JRNL REF BIOCHEMISTRY V. 65 297 2026 JRNL REFN ISSN 0006-2960 JRNL PMID 41566164 JRNL DOI 10.1021/ACS.BIOCHEM.5C00616 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 9GRM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-SEP-24. REMARK 100 THE DEPOSITION ID IS D_1292141666. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 200 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.48 MM [U-100% 15N] CDC42, 0.58 REMARK 210 MM NONE PEPTIDE, 50 MM NONE REMARK 210 SODIUM PHOSPHATE, 150 MM NONE REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 0.4 MM [U-13C; U-15N] CDC42, REMARK 210 0.45 MM NONE PEPTIDE, 50 MM NONE REMARK 210 SODIUM PHOSPHATE, 150 MM NONE REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 0.415 MM [U-100% 15N] PEPTIDE, REMARK 210 0.45 MM NONE CDC42, 50 MM NONE REMARK 210 SODIUM PHOSPHATE, 150 MM NONE REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 2D 1H-13C HSQC; REMARK 210 3D HNCA; 3D HN(CO)CA; 3D HNCACB; REMARK 210 3D HN(COCA)CB; 3D HCCH-TOCSY; 3D REMARK 210 1H-13C NOESY; 3D X-FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2.4, ARIA REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 24 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: DIMERIC 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 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 HZ1 LYS A 153 OE1 GLU A 171 1.57 REMARK 500 OD2 ASP A 170 HE2 HIS B 5 1.60 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 THR A 35 142.58 83.76 REMARK 500 1 VAL A 36 119.86 -169.85 REMARK 500 1 ARG A 68 -158.45 41.63 REMARK 500 1 PRO A 69 -7.59 -48.38 REMARK 500 1 LYS A 150 61.74 64.73 REMARK 500 1 PRO B 12 -149.10 -80.46 REMARK 500 2 ALA A 13 46.01 39.81 REMARK 500 2 VAL A 33 127.51 -38.69 REMARK 500 2 THR A 35 108.29 -4.15 REMARK 500 2 PHE A 37 114.55 -161.19 REMARK 500 2 THR A 58 -156.40 -137.38 REMARK 500 2 ALA A 59 -50.04 78.57 REMARK 500 2 TYR A 72 86.37 -157.62 REMARK 500 2 THR A 75 132.61 -39.45 REMARK 500 2 GLN A 116 35.85 74.92 REMARK 500 2 PRO B 12 -136.31 -80.75 REMARK 500 3 VAL A 14 -85.93 -85.31 REMARK 500 3 GLU A 31 -167.16 49.26 REMARK 500 3 TYR A 32 -75.44 -110.45 REMARK 500 3 VAL A 33 130.02 65.59 REMARK 500 3 THR A 35 -79.48 61.36 REMARK 500 3 VAL A 36 70.06 34.38 REMARK 500 3 PHE A 37 -63.16 -146.39 REMARK 500 3 ASP A 38 -42.61 165.93 REMARK 500 3 ASN A 39 -107.20 81.81 REMARK 500 3 TYR A 72 56.35 -147.42 REMARK 500 3 LYS A 96 -44.56 -133.89 REMARK 500 3 LYS A 150 62.22 65.07 REMARK 500 3 GLU A 181 84.39 63.23 REMARK 500 3 HIS B 5 72.07 -102.93 REMARK 500 3 ASP B 10 -71.15 -61.57 REMARK 500 3 PRO B 12 -85.80 -76.77 REMARK 500 4 VAL A 33 123.68 59.89 REMARK 500 4 THR A 35 -74.38 81.28 REMARK 500 4 VAL A 36 -42.95 54.54 REMARK 500 4 ASP A 38 71.64 -108.88 REMARK 500 4 ARG A 68 -175.92 57.36 REMARK 500 4 PRO A 69 -6.93 -47.27 REMARK 500 4 LYS A 96 -69.42 -108.17 REMARK 500 4 GLN A 162 -4.82 69.25 REMARK 500 4 GLU A 181 104.91 69.50 REMARK 500 4 PRO B 12 -80.83 -74.88 REMARK 500 5 GLU A 31 -153.48 46.91 REMARK 500 5 VAL A 33 124.57 61.81 REMARK 500 5 THR A 35 126.20 74.61 REMARK 500 5 VAL A 36 105.35 -160.34 REMARK 500 5 ARG A 68 178.90 58.36 REMARK 500 5 PRO A 69 -5.73 -41.09 REMARK 500 5 LYS A 96 -69.99 -108.13 REMARK 500 5 GLU A 181 103.98 71.07 REMARK 500 REMARK 500 THIS ENTRY HAS 264 RAMACHANDRAN OUTLIERS. 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 MG A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 17 OG1 REMARK 620 2 THR A 35 OG1 107.2 REMARK 620 3 GNP A 201 O2G 167.7 80.7 REMARK 620 4 GNP A 201 O2B 88.9 163.8 83.8 REMARK 620 5 HOH A 301 O 97.7 85.8 92.2 90.4 REMARK 620 6 HOH A 302 O 81.5 93.4 88.7 90.6 178.7 REMARK 620 N 1 2 3 4 5 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34958 RELATED DB: BMRB REMARK 900 CDC42 IN COMPLEX WITH INHIBITORY PEPTIDE DBREF 9GRM A 1 184 UNP P60953 CDC42_HUMAN 1 184 DBREF 9GRM B 1 16 PDB 9GRM 9GRM 1 16 SEQADV 9GRM LEU A 61 UNP P60953 GLN 61 ENGINEERED MUTATION SEQRES 1 A 184 MET GLN THR ILE LYS CYS VAL VAL VAL GLY ASP GLY ALA SEQRES 2 A 184 VAL GLY LYS THR CYS LEU LEU ILE SER TYR THR THR ASN SEQRES 3 A 184 LYS PHE PRO SER GLU TYR VAL PRO THR VAL PHE ASP ASN SEQRES 4 A 184 TYR ALA VAL THR VAL MET ILE GLY GLY GLU PRO TYR THR SEQRES 5 A 184 LEU GLY LEU PHE ASP THR ALA GLY LEU GLU ASP TYR ASP SEQRES 6 A 184 ARG LEU ARG PRO LEU SER TYR PRO GLN THR ASP VAL PHE SEQRES 7 A 184 LEU VAL CYS PHE SER VAL VAL SER PRO SER SER PHE GLU SEQRES 8 A 184 ASN VAL LYS GLU LYS TRP VAL PRO GLU ILE THR HIS HIS SEQRES 9 A 184 CYS PRO LYS THR PRO PHE LEU LEU VAL GLY THR GLN ILE SEQRES 10 A 184 ASP LEU ARG ASP ASP PRO SER THR ILE GLU LYS LEU ALA SEQRES 11 A 184 LYS ASN LYS GLN LYS PRO ILE THR PRO GLU THR ALA GLU SEQRES 12 A 184 LYS LEU ALA ARG ASP LEU LYS ALA VAL LYS TYR VAL GLU SEQRES 13 A 184 CYS SER ALA LEU THR GLN LYS GLY LEU LYS ASN VAL PHE SEQRES 14 A 184 ASP GLU ALA ILE LEU ALA ALA LEU GLU PRO PRO GLU PRO SEQRES 15 A 184 LYS LYS SEQRES 1 B 16 PRO SER ILE CYS HIS VAL HIS ARG PRO ASP TRP PRO CYS SEQRES 2 B 16 ALA TYR ARG HET GNP A 201 45 HET MG A 202 1 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION FORMUL 3 GNP C10 H17 N6 O13 P3 FORMUL 4 MG MG 2+ FORMUL 5 HOH *2(H2 O) HELIX 1 AA1 GLY A 15 THR A 25 1 11 HELIX 2 AA2 LEU A 61 ASP A 65 5 5 HELIX 3 AA3 LEU A 67 TYR A 72 5 6 HELIX 4 AA4 SER A 86 LYS A 96 1 11 HELIX 5 AA5 LYS A 96 CYS A 105 1 10 HELIX 6 AA6 ILE A 117 ARG A 120 5 4 HELIX 7 AA7 ASP A 122 ASN A 132 1 11 HELIX 8 AA8 THR A 138 LYS A 150 1 13 HELIX 9 AA9 GLY A 164 GLU A 178 1 15 SHEET 1 AA1 8 TYR A 154 CYS A 157 0 SHEET 2 AA1 8 PHE A 110 THR A 115 1 N GLY A 114 O VAL A 155 SHEET 3 AA1 8 VAL A 77 SER A 83 1 N PHE A 78 O LEU A 111 SHEET 4 AA1 8 GLN A 2 GLY A 10 1 N VAL A 7 O LEU A 79 SHEET 5 AA1 8 GLU A 49 ASP A 57 1 O GLY A 54 N ILE A 4 SHEET 6 AA1 8 ASP A 38 ILE A 46 -1 N VAL A 42 O LEU A 53 SHEET 7 AA1 8 SER B 2 CYS B 4 -1 O CYS B 4 N MET A 45 SHEET 8 AA1 8 CYS B 13 TYR B 15 -1 O ALA B 14 N ILE B 3 SSBOND 1 CYS B 4 CYS B 13 1555 1555 2.03 LINK OG1 THR A 17 MG MG A 202 1555 1555 2.31 LINK OG1 THR A 35 MG MG A 202 1555 1555 2.27 LINK O2G GNP A 201 MG MG A 202 1555 1555 2.29 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.29 LINK MG MG A 202 O HOH A 301 1555 1555 2.30 LINK MG MG A 202 O HOH A 302 1555 1555 2.30 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 MODEL 1 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MODEL 21 ENDMDL MODEL 22 ENDMDL MODEL 23 ENDMDL MODEL 24 ENDMDL CONECT 237 3209 CONECT 526 3209 CONECT 2952 3102 CONECT 3102 2952 CONECT 3164 3165 3166 3167 3168 CONECT 3165 3164 CONECT 3166 3164 3209 CONECT 3167 3164 CONECT 3168 3164 3169 3196 CONECT 3169 3168 3170 3171 3172 CONECT 3170 3169 CONECT 3171 3169 3209 CONECT 3172 3169 3173 CONECT 3173 3172 3174 3175 3176 CONECT 3174 3173 CONECT 3175 3173 CONECT 3176 3173 3177 CONECT 3177 3176 3178 3197 3198 CONECT 3178 3177 3179 3180 3199 CONECT 3179 3178 3184 CONECT 3180 3178 3181 3182 3200 CONECT 3181 3180 3201 CONECT 3182 3180 3183 3184 3202 CONECT 3183 3182 3203 CONECT 3184 3179 3182 3185 3204 CONECT 3185 3184 3186 3195 CONECT 3186 3185 3187 3205 CONECT 3187 3186 3188 CONECT 3188 3187 3189 3195 CONECT 3189 3188 3190 3191 CONECT 3190 3189 CONECT 3191 3189 3192 3206 CONECT 3192 3191 3193 3194 CONECT 3193 3192 3207 3208 CONECT 3194 3192 3195 CONECT 3195 3185 3188 3194 CONECT 3196 3168 CONECT 3197 3177 CONECT 3198 3177 CONECT 3199 3178 CONECT 3200 3180 CONECT 3201 3181 CONECT 3202 3182 CONECT 3203 3183 CONECT 3204 3184 CONECT 3205 3186 CONECT 3206 3191 CONECT 3207 3193 CONECT 3208 3193 CONECT 3209 237 526 3166 3171 CONECT 3209 3210 3213 CONECT 3210 3209 CONECT 3213 3209 MASTER 178 0 2 9 8 0 0 6 1607 2 53 17 END