PDB Short entry for 5YXH HEADER SIGNALING PROTEIN 05-DEC-17 5YXH TITLE STRUCTURE OF RHEB-GDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP-BINDING PROTEIN RHEB; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: RAS HOMOLOG ENRICHED IN BRAIN; COMPND 5 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: RHEB, RHEB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GTPASE, MTORC1 SIGNALING, RHEB, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.J.MAHONEY REVDAT 2 22-NOV-23 5YXH 1 LINK REVDAT 1 28-FEB-18 5YXH 0 JRNL AUTH S.J.MAHONEY,S.NARAYAN,L.MOLZ,L.A.BERSTLER,S.A.KANG, JRNL AUTH 2 G.P.VLASUK,E.SAIAH JRNL TITL A SMALL MOLECULE INHIBITOR OF RHEB SELECTIVELY TARGETS JRNL TITL 2 MTORC1 SIGNALING. JRNL REF NAT COMMUN V. 9 548 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29416044 JRNL DOI 10.1038/S41467-018-03035-Z REMARK 2 REMARK 2 RESOLUTION. 2.04 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.04 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 59.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 36174 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.246 REMARK 3 R VALUE (WORKING SET) : 0.244 REMARK 3 FREE R VALUE : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1807 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.04 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2577 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 125 REMARK 3 BIN FREE R VALUE : 0.3760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5161 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 116 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.17000 REMARK 3 B22 (A**2) : 1.54000 REMARK 3 B33 (A**2) : -1.48000 REMARK 3 B12 (A**2) : 0.78000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : -0.22000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.319 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.247 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.226 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.541 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.930 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.888 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5380 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5167 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7241 ; 1.167 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11901 ; 0.729 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 642 ; 6.144 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 234 ;38.670 ;25.256 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 987 ;14.492 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.299 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 838 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5865 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1167 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2595 ; 1.738 ; 4.025 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2594 ; 1.738 ; 4.025 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3228 ; 3.106 ; 6.013 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3229 ; 3.106 ; 6.013 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2785 ; 1.278 ; 4.177 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2760 ; 1.267 ; 4.181 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4001 ; 2.248 ; 6.222 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6037 ; 5.189 ;31.510 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6010 ; 5.167 ;31.491 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5YXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-17. REMARK 100 THE DEPOSITION ID IS D_1300006027. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JAN-15 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37982 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.040 REMARK 200 RESOLUTION RANGE LOW (A) : 59.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.04 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 1XTQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% W/V PEG 1500, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 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 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 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 SER A 1 REMARK 465 PRO A 2 REMARK 465 LYS A 109 REMARK 465 VAL A 110 REMARK 465 GLN A 111 REMARK 465 ILE A 112 REMARK 465 SER B 1 REMARK 465 PRO B 2 REMARK 465 PHE B 70 REMARK 465 PRO B 71 REMARK 465 GLN B 72 REMARK 465 THR B 73 REMARK 465 TYR B 74 REMARK 465 SER C 1 REMARK 465 PRO C 2 REMARK 465 ILE C 69 REMARK 465 PHE C 70 REMARK 465 PRO C 71 REMARK 465 GLN C 72 REMARK 465 THR C 73 REMARK 465 TYR C 74 REMARK 465 SER C 75 REMARK 465 ILE C 76 REMARK 465 LYS C 109 REMARK 465 VAL C 110 REMARK 465 GLN C 111 REMARK 465 ILE C 112 REMARK 465 SER D 1 REMARK 465 PRO D 2 REMARK 465 PRO D 71 REMARK 465 GLN D 72 REMARK 465 THR D 73 REMARK 465 TYR D 74 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 ASP A 65 -159.98 -135.67 REMARK 500 VAL A 107 -49.16 -131.58 REMARK 500 ASP B 105 -60.44 -102.75 REMARK 500 GLN B 111 73.40 63.50 REMARK 500 TYR C 67 43.42 -101.22 REMARK 500 SER D 68 120.12 -36.94 REMARK 500 ASP D 77 29.73 42.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH C 337 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH C 338 DISTANCE = 6.84 ANGSTROMS 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 SER A 20 OG REMARK 620 2 GDP A 201 O1B 89.5 REMARK 620 3 HOH A 301 O 66.0 89.6 REMARK 620 4 HOH A 310 O 102.0 98.9 165.4 REMARK 620 5 HOH A 313 O 151.7 93.5 85.8 105.3 REMARK 620 6 HOH A 317 O 77.6 162.8 74.8 94.9 92.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER B 20 OG REMARK 620 2 GDP B 201 O3B 82.4 REMARK 620 3 HOH B 302 O 88.4 82.1 REMARK 620 4 HOH B 303 O 150.3 96.6 121.0 REMARK 620 5 HOH B 310 O 75.5 84.5 160.3 74.8 REMARK 620 6 HOH B 323 O 94.3 159.7 117.9 76.3 75.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 20 OG REMARK 620 2 GDP C 201 O1B 89.4 REMARK 620 3 HOH C 303 O 98.8 87.8 REMARK 620 4 HOH C 308 O 156.0 89.7 105.2 REMARK 620 5 HOH C 312 O 84.0 87.4 174.4 71.9 REMARK 620 6 HOH C 322 O 89.2 170.9 101.3 87.9 83.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER D 20 OG REMARK 620 2 GDP D 201 O3B 89.4 REMARK 620 3 HOH D 301 O 97.9 101.2 REMARK 620 4 HOH D 305 O 90.1 75.9 171.5 REMARK 620 5 HOH D 311 O 174.1 96.2 79.2 93.1 REMARK 620 6 HOH D 330 O 90.8 177.6 81.1 101.7 83.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 202 DBREF 5YXH A 2 169 UNP Q15382 RHEB_HUMAN 2 169 DBREF 5YXH B 2 169 UNP Q15382 RHEB_HUMAN 2 169 DBREF 5YXH C 2 169 UNP Q15382 RHEB_HUMAN 2 169 DBREF 5YXH D 2 169 UNP Q15382 RHEB_HUMAN 2 169 SEQADV 5YXH SER A 1 UNP Q15382 EXPRESSION TAG SEQADV 5YXH LEU A 170 UNP Q15382 EXPRESSION TAG SEQADV 5YXH GLU A 171 UNP Q15382 EXPRESSION TAG SEQADV 5YXH SER B 1 UNP Q15382 EXPRESSION TAG SEQADV 5YXH LEU B 170 UNP Q15382 EXPRESSION TAG SEQADV 5YXH GLU B 171 UNP Q15382 EXPRESSION TAG SEQADV 5YXH SER C 1 UNP Q15382 EXPRESSION TAG SEQADV 5YXH LEU C 170 UNP Q15382 EXPRESSION TAG SEQADV 5YXH GLU C 171 UNP Q15382 EXPRESSION TAG SEQADV 5YXH SER D 1 UNP Q15382 EXPRESSION TAG SEQADV 5YXH LEU D 170 UNP Q15382 EXPRESSION TAG SEQADV 5YXH GLU D 171 UNP Q15382 EXPRESSION TAG SEQRES 1 A 171 SER PRO GLN SER LYS SER ARG LYS ILE ALA ILE LEU GLY SEQRES 2 A 171 TYR ARG SER VAL GLY LYS SER SER LEU THR ILE GLN PHE SEQRES 3 A 171 VAL GLU GLY GLN PHE VAL ASP SER TYR ASP PRO THR ILE SEQRES 4 A 171 GLU ASN THR PHE THR LYS LEU ILE THR VAL ASN GLY GLN SEQRES 5 A 171 GLU TYR HIS LEU GLN LEU VAL ASP THR ALA GLY GLN ASP SEQRES 6 A 171 GLU TYR SER ILE PHE PRO GLN THR TYR SER ILE ASP ILE SEQRES 7 A 171 ASN GLY TYR ILE LEU VAL TYR SER VAL THR SER ILE LYS SEQRES 8 A 171 SER PHE GLU VAL ILE LYS VAL ILE HIS GLY LYS LEU LEU SEQRES 9 A 171 ASP MET VAL GLY LYS VAL GLN ILE PRO ILE MET LEU VAL SEQRES 10 A 171 GLY ASN LYS LYS ASP LEU HIS MET GLU ARG VAL ILE SER SEQRES 11 A 171 TYR GLU GLU GLY LYS ALA LEU ALA GLU SER TRP ASN ALA SEQRES 12 A 171 ALA PHE LEU GLU SER SER ALA LYS GLU ASN GLN THR ALA SEQRES 13 A 171 VAL ASP VAL PHE ARG ARG ILE ILE LEU GLU ALA GLU LYS SEQRES 14 A 171 LEU GLU SEQRES 1 B 171 SER PRO GLN SER LYS SER ARG LYS ILE ALA ILE LEU GLY SEQRES 2 B 171 TYR ARG SER VAL GLY LYS SER SER LEU THR ILE GLN PHE SEQRES 3 B 171 VAL GLU GLY GLN PHE VAL ASP SER TYR ASP PRO THR ILE SEQRES 4 B 171 GLU ASN THR PHE THR LYS LEU ILE THR VAL ASN GLY GLN SEQRES 5 B 171 GLU TYR HIS LEU GLN LEU VAL ASP THR ALA GLY GLN ASP SEQRES 6 B 171 GLU TYR SER ILE PHE PRO GLN THR TYR SER ILE ASP ILE SEQRES 7 B 171 ASN GLY TYR ILE LEU VAL TYR SER VAL THR SER ILE LYS SEQRES 8 B 171 SER PHE GLU VAL ILE LYS VAL ILE HIS GLY LYS LEU LEU SEQRES 9 B 171 ASP MET VAL GLY LYS VAL GLN ILE PRO ILE MET LEU VAL SEQRES 10 B 171 GLY ASN LYS LYS ASP LEU HIS MET GLU ARG VAL ILE SER SEQRES 11 B 171 TYR GLU GLU GLY LYS ALA LEU ALA GLU SER TRP ASN ALA SEQRES 12 B 171 ALA PHE LEU GLU SER SER ALA LYS GLU ASN GLN THR ALA SEQRES 13 B 171 VAL ASP VAL PHE ARG ARG ILE ILE LEU GLU ALA GLU LYS SEQRES 14 B 171 LEU GLU SEQRES 1 C 171 SER PRO GLN SER LYS SER ARG LYS ILE ALA ILE LEU GLY SEQRES 2 C 171 TYR ARG SER VAL GLY LYS SER SER LEU THR ILE GLN PHE SEQRES 3 C 171 VAL GLU GLY GLN PHE VAL ASP SER TYR ASP PRO THR ILE SEQRES 4 C 171 GLU ASN THR PHE THR LYS LEU ILE THR VAL ASN GLY GLN SEQRES 5 C 171 GLU TYR HIS LEU GLN LEU VAL ASP THR ALA GLY GLN ASP SEQRES 6 C 171 GLU TYR SER ILE PHE PRO GLN THR TYR SER ILE ASP ILE SEQRES 7 C 171 ASN GLY TYR ILE LEU VAL TYR SER VAL THR SER ILE LYS SEQRES 8 C 171 SER PHE GLU VAL ILE LYS VAL ILE HIS GLY LYS LEU LEU SEQRES 9 C 171 ASP MET VAL GLY LYS VAL GLN ILE PRO ILE MET LEU VAL SEQRES 10 C 171 GLY ASN LYS LYS ASP LEU HIS MET GLU ARG VAL ILE SER SEQRES 11 C 171 TYR GLU GLU GLY LYS ALA LEU ALA GLU SER TRP ASN ALA SEQRES 12 C 171 ALA PHE LEU GLU SER SER ALA LYS GLU ASN GLN THR ALA SEQRES 13 C 171 VAL ASP VAL PHE ARG ARG ILE ILE LEU GLU ALA GLU LYS SEQRES 14 C 171 LEU GLU SEQRES 1 D 171 SER PRO GLN SER LYS SER ARG LYS ILE ALA ILE LEU GLY SEQRES 2 D 171 TYR ARG SER VAL GLY LYS SER SER LEU THR ILE GLN PHE SEQRES 3 D 171 VAL GLU GLY GLN PHE VAL ASP SER TYR ASP PRO THR ILE SEQRES 4 D 171 GLU ASN THR PHE THR LYS LEU ILE THR VAL ASN GLY GLN SEQRES 5 D 171 GLU TYR HIS LEU GLN LEU VAL ASP THR ALA GLY GLN ASP SEQRES 6 D 171 GLU TYR SER ILE PHE PRO GLN THR TYR SER ILE ASP ILE SEQRES 7 D 171 ASN GLY TYR ILE LEU VAL TYR SER VAL THR SER ILE LYS SEQRES 8 D 171 SER PHE GLU VAL ILE LYS VAL ILE HIS GLY LYS LEU LEU SEQRES 9 D 171 ASP MET VAL GLY LYS VAL GLN ILE PRO ILE MET LEU VAL SEQRES 10 D 171 GLY ASN LYS LYS ASP LEU HIS MET GLU ARG VAL ILE SER SEQRES 11 D 171 TYR GLU GLU GLY LYS ALA LEU ALA GLU SER TRP ASN ALA SEQRES 12 D 171 ALA PHE LEU GLU SER SER ALA LYS GLU ASN GLN THR ALA SEQRES 13 D 171 VAL ASP VAL PHE ARG ARG ILE ILE LEU GLU ALA GLU LYS SEQRES 14 D 171 LEU GLU HET GDP A 201 28 HET MG A 202 1 HET GDP B 201 28 HET MG B 202 1 HET GDP C 201 28 HET MG C 202 1 HET GDP D 201 28 HET MG D 202 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 GDP 4(C10 H15 N5 O11 P2) FORMUL 6 MG 4(MG 2+) FORMUL 13 HOH *147(H2 O) HELIX 1 AA1 GLY A 18 GLY A 29 1 12 HELIX 2 AA2 PRO A 71 SER A 75 5 5 HELIX 3 AA3 SER A 89 MET A 106 1 18 HELIX 4 AA4 SER A 130 ASN A 142 1 13 HELIX 5 AA5 GLU A 152 GLU A 171 1 20 HELIX 6 AA6 GLY B 18 GLY B 29 1 12 HELIX 7 AA7 SER B 89 VAL B 107 1 19 HELIX 8 AA8 SER B 130 TRP B 141 1 12 HELIX 9 AA9 GLU B 152 GLU B 171 1 20 HELIX 10 AB1 GLY C 18 GLY C 29 1 12 HELIX 11 AB2 SER C 89 GLY C 108 1 20 HELIX 12 AB3 SER C 130 TRP C 141 1 12 HELIX 13 AB4 GLU C 152 GLU C 171 1 20 HELIX 14 AB5 GLY D 18 GLY D 29 1 12 HELIX 15 AB6 SER D 89 VAL D 107 1 19 HELIX 16 AB7 SER D 130 ASN D 142 1 13 HELIX 17 AB8 GLU D 152 GLU D 171 1 20 SHEET 1 AA1 6 ASN A 41 VAL A 49 0 SHEET 2 AA1 6 GLN A 52 ASP A 60 -1 O LEU A 58 N PHE A 43 SHEET 3 AA1 6 LYS A 5 GLY A 13 1 N ILE A 9 O VAL A 59 SHEET 4 AA1 6 GLY A 80 SER A 86 1 O ILE A 82 N LEU A 12 SHEET 5 AA1 6 ILE A 114 ASN A 119 1 O VAL A 117 N LEU A 83 SHEET 6 AA1 6 ALA A 144 GLU A 147 1 O ALA A 144 N LEU A 116 SHEET 1 AA2 6 ASN B 41 VAL B 49 0 SHEET 2 AA2 6 GLN B 52 ASP B 60 -1 O LEU B 58 N PHE B 43 SHEET 3 AA2 6 SER B 6 GLY B 13 1 N ILE B 9 O GLN B 57 SHEET 4 AA2 6 GLY B 80 SER B 86 1 O VAL B 84 N LEU B 12 SHEET 5 AA2 6 ILE B 114 ASN B 119 1 O ASN B 119 N TYR B 85 SHEET 6 AA2 6 PHE B 145 GLU B 147 1 O LEU B 146 N GLY B 118 SHEET 1 AA3 6 ASN C 41 VAL C 49 0 SHEET 2 AA3 6 GLN C 52 ASP C 60 -1 O LEU C 58 N PHE C 43 SHEET 3 AA3 6 LYS C 5 GLY C 13 1 N ILE C 9 O VAL C 59 SHEET 4 AA3 6 GLY C 80 SER C 86 1 O VAL C 84 N LEU C 12 SHEET 5 AA3 6 ILE C 114 ASN C 119 1 O ASN C 119 N TYR C 85 SHEET 6 AA3 6 PHE C 145 SER C 148 1 O SER C 148 N GLY C 118 SHEET 1 AA4 6 ASN D 41 VAL D 49 0 SHEET 2 AA4 6 GLN D 52 ASP D 60 -1 O LEU D 58 N PHE D 43 SHEET 3 AA4 6 LYS D 5 GLY D 13 1 N LYS D 5 O HIS D 55 SHEET 4 AA4 6 GLY D 80 SER D 86 1 O ILE D 82 N LEU D 12 SHEET 5 AA4 6 ILE D 114 ASN D 119 1 O ASN D 119 N TYR D 85 SHEET 6 AA4 6 PHE D 145 GLU D 147 1 O LEU D 146 N GLY D 118 LINK OG SER A 20 MG MG A 202 1555 1555 2.18 LINK O1B GDP A 201 MG MG A 202 1555 1555 2.18 LINK MG MG A 202 O HOH A 301 1555 1555 2.17 LINK MG MG A 202 O HOH A 310 1555 1555 2.17 LINK MG MG A 202 O HOH A 313 1555 1555 2.17 LINK MG MG A 202 O HOH A 317 1555 1555 2.18 LINK OG SER B 20 MG MG B 202 1555 1555 2.18 LINK O3B GDP B 201 MG MG B 202 1555 1555 2.18 LINK MG MG B 202 O HOH B 302 1555 1555 2.16 LINK MG MG B 202 O HOH B 303 1555 1555 2.17 LINK MG MG B 202 O HOH B 310 1555 1555 2.18 LINK MG MG B 202 O HOH B 323 1555 1555 2.18 LINK OG SER C 20 MG MG C 202 1555 1555 2.17 LINK O1B GDP C 201 MG MG C 202 1555 1555 2.18 LINK MG MG C 202 O HOH C 303 1555 1555 2.17 LINK MG MG C 202 O HOH C 308 1555 1555 2.17 LINK MG MG C 202 O HOH C 312 1555 1555 2.17 LINK MG MG C 202 O HOH C 322 1555 1555 2.18 LINK OG SER D 20 MG MG D 202 1555 1555 2.17 LINK O3B GDP D 201 MG MG D 202 1555 1555 2.17 LINK MG MG D 202 O HOH D 301 1555 1555 2.17 LINK MG MG D 202 O HOH D 305 1555 1555 2.17 LINK MG MG D 202 O HOH D 311 1555 1555 2.17 LINK MG MG D 202 O HOH D 330 1555 1555 2.18 SITE 1 AC1 20 SER A 16 VAL A 17 GLY A 18 LYS A 19 SITE 2 AC1 20 SER A 20 SER A 21 PHE A 31 VAL A 32 SITE 3 AC1 20 ASP A 33 ASN A 119 LYS A 120 ASP A 122 SITE 4 AC1 20 LEU A 123 SER A 149 ALA A 150 LYS A 151 SITE 5 AC1 20 MG A 202 HOH A 301 HOH A 310 HOH A 313 SITE 1 AC2 6 SER A 20 GDP A 201 HOH A 301 HOH A 310 SITE 2 AC2 6 HOH A 313 HOH A 317 SITE 1 AC3 20 SER B 16 VAL B 17 GLY B 18 LYS B 19 SITE 2 AC3 20 SER B 20 SER B 21 PHE B 31 VAL B 32 SITE 3 AC3 20 ASP B 33 ASN B 119 LYS B 120 ASP B 122 SITE 4 AC3 20 LEU B 123 SER B 149 ALA B 150 MG B 202 SITE 5 AC3 20 HOH B 302 HOH B 303 HOH B 310 HOH B 319 SITE 1 AC4 6 SER B 20 GDP B 201 HOH B 302 HOH B 303 SITE 2 AC4 6 HOH B 310 HOH B 323 SITE 1 AC5 20 SER C 16 VAL C 17 GLY C 18 LYS C 19 SITE 2 AC5 20 SER C 20 SER C 21 PHE C 31 VAL C 32 SITE 3 AC5 20 ASN C 119 LYS C 120 ASP C 122 LEU C 123 SITE 4 AC5 20 SER C 149 ALA C 150 LYS C 151 MG C 202 SITE 5 AC5 20 HOH C 303 HOH C 308 HOH C 312 HOH C 321 SITE 1 AC6 6 SER C 20 GDP C 201 HOH C 303 HOH C 308 SITE 2 AC6 6 HOH C 312 HOH C 322 SITE 1 AC7 18 SER D 16 VAL D 17 GLY D 18 LYS D 19 SITE 2 AC7 18 SER D 20 SER D 21 PHE D 31 VAL D 32 SITE 3 AC7 18 ASP D 33 ASN D 119 LYS D 120 ASP D 122 SITE 4 AC7 18 LEU D 123 SER D 149 ALA D 150 MG D 202 SITE 5 AC7 18 HOH D 305 HOH D 311 SITE 1 AC8 6 SER D 20 GDP D 201 HOH D 301 HOH D 305 SITE 2 AC8 6 HOH D 311 HOH D 330 CRYST1 50.166 58.963 64.345 110.53 90.03 108.16 P 1 4 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 0.019934 0.006538 0.002608 0.00000 SCALE2 0.000000 0.017849 0.007093 0.00000 SCALE3 0.000000 0.000000 0.016723 0.00000