PDB Short entry for 5KTY HEADER HYDROLASE 12-JUL-16 5KTY TITLE HMIRO EF HAND AND CGTPASE DOMAINS, GDP AND CA2+ BOUND STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MITOCHONDRIAL RHO GTPASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HAND AND CGTPASE DOMAINS (UNP RESIDUES 177-592); COMPND 5 SYNONYM: HMIRO-1, RAC-GTP-BINDING PROTEIN-LIKE PROTEIN, RAS HOMOLOG COMPND 6 GENE FAMILY MEMBER T1; COMPND 7 EC: 3.6.5.-; COMPND 8 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: RHOT1, ARHT1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MIRO, GTPASE, PARKIN, MITOCHONDRIA, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.L.KLOSOWIAK,P.J.FOCIA,S.E.RICE,D.M.FREYMANN REVDAT 2 04-OCT-23 5KTY 1 REMARK LINK REVDAT 1 21-SEP-16 5KTY 0 JRNL AUTH J.L.KLOSOWIAK,S.PARK,K.P.SMITH,M.E.FRENCH,P.J.FOCIA, JRNL AUTH 2 D.M.FREYMANN,S.E.RICE JRNL TITL STRUCTURAL INSIGHTS INTO PARKIN SUBSTRATE LYSINE TARGETING JRNL TITL 2 FROM MINIMAL MIRO SUBSTRATES. JRNL REF SCI REP V. 6 33019 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27605430 JRNL DOI 10.1038/SREP33019 REMARK 2 REMARK 2 RESOLUTION. 2.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.17 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 20490 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.190 REMARK 3 FREE R VALUE TEST SET COUNT : 1884 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 29.1758 - 5.9145 1.00 1676 170 0.1669 0.1957 REMARK 3 2 5.9145 - 4.7008 1.00 1569 159 0.1813 0.2312 REMARK 3 3 4.7008 - 4.1085 1.00 1526 156 0.1592 0.1935 REMARK 3 4 4.1085 - 3.7337 1.00 1524 155 0.1802 0.2256 REMARK 3 5 3.7337 - 3.4665 0.99 1494 153 0.2214 0.2155 REMARK 3 6 3.4665 - 3.2624 0.98 1476 148 0.2388 0.2901 REMARK 3 7 3.2624 - 3.0992 0.97 1466 149 0.2561 0.3375 REMARK 3 8 3.0992 - 2.9644 0.95 1394 143 0.2757 0.3098 REMARK 3 9 2.9644 - 2.8504 0.93 1404 140 0.2846 0.3786 REMARK 3 10 2.8504 - 2.7521 0.91 1330 134 0.2797 0.3414 REMARK 3 11 2.7521 - 2.6661 0.88 1319 131 0.2784 0.3249 REMARK 3 12 2.6661 - 2.5900 0.84 1255 125 0.3181 0.3423 REMARK 3 13 2.5900 - 2.5218 0.79 1173 121 0.3379 0.3958 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.004 3380 REMARK 3 ANGLE : 0.675 4580 REMARK 3 CHIRALITY : 0.026 503 REMARK 3 PLANARITY : 0.003 576 REMARK 3 DIHEDRAL : 12.285 1252 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 5KTY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-JUL-16. REMARK 100 THE DEPOSITION ID IS D_1000222745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-FEB-14 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 : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21762 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 4C0L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MG/ML PROTEIN, 5 MM CALCIUM REMARK 280 CHLORIDE, 1 MM GDP, 0.04 M POTASSIUM PHOSPHATE, 16% W/V PEG8000, REMARK 280 20% V/V GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 111.08750 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.03650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.03650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 166.63125 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.03650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.03650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.54375 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.03650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.03650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 166.63125 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.03650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.03650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.54375 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 111.08750 REMARK 290 REMARK 290 REMARK: NULL 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: 1520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -41.0 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 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 GLU A 177 REMARK 465 GLU A 178 REMARK 465 LYS A 179 REMARK 465 GLU A 180 REMARK 465 GLN A 260 REMARK 465 ARG A 261 REMARK 465 GLY A 262 REMARK 465 ARG A 263 REMARK 465 HIS A 264 REMARK 465 THR A 583 REMARK 465 GLN A 584 REMARK 465 ALA A 585 REMARK 465 ASP A 586 REMARK 465 LEU A 587 REMARK 465 LYS A 588 REMARK 465 SER A 589 REMARK 465 SER A 590 REMARK 465 THR A 591 REMARK 465 PHE A 592 REMARK 465 LEU A 593 REMARK 465 GLU A 594 REMARK 465 HIS A 595 REMARK 465 HIS A 596 REMARK 465 HIS A 597 REMARK 465 HIS A 598 REMARK 465 HIS A 599 REMARK 465 HIS A 600 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 376 O GLU A 480 7556 2.02 REMARK 500 NH2 ARG A 376 OE2 GLU A 480 7556 2.16 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 PHE A 217 -107.59 -124.25 REMARK 500 ASN A 218 -57.77 -149.24 REMARK 500 PRO A 220 109.80 -54.82 REMARK 500 LEU A 221 165.29 -48.10 REMARK 500 HIS A 236 -41.21 -133.36 REMARK 500 ASP A 277 -162.06 -102.54 REMARK 500 ASN A 352 -158.33 -86.72 REMARK 500 ARG A 450 -169.25 -100.12 REMARK 500 GLU A 451 -97.61 -19.15 REMARK 500 ASP A 517 53.41 -104.70 REMARK 500 ASP A 563 -152.75 -98.92 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 CA A 704 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 197 OD1 REMARK 620 2 ASP A 199 OD1 77.4 REMARK 620 3 ASP A 201 OD1 74.7 72.6 REMARK 620 4 THR A 203 O 84.0 152.7 83.3 REMARK 620 5 GLU A 208 OE1 111.9 117.2 168.7 88.3 REMARK 620 6 GLU A 208 OE2 98.1 64.8 137.3 138.7 52.5 REMARK 620 7 HOH A 829 O 159.3 108.1 87.8 83.0 83.8 102.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 705 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 317 OD1 REMARK 620 2 ASP A 319 OD1 80.8 REMARK 620 3 ASP A 319 OD2 122.4 43.1 REMARK 620 4 ASP A 321 OD1 78.7 68.7 89.1 REMARK 620 5 ALA A 323 O 90.8 150.1 143.0 81.5 REMARK 620 6 GLU A 328 OE1 110.0 125.9 97.4 163.2 84.0 REMARK 620 7 GLU A 328 OE2 93.8 74.9 64.7 143.5 134.6 52.2 REMARK 620 8 HOH A 819 O 155.6 94.6 61.7 77.3 81.3 92.2 108.2 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 702 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 428 OD1 REMARK 620 2 GDP A 701 O3B 85.4 REMARK 620 3 GDP A 703 O3B 160.7 75.8 REMARK 620 4 GDP A 703 O1A 96.3 80.3 85.5 REMARK 620 5 HOH A 802 O 85.1 61.3 81.6 141.5 REMARK 620 N 1 2 3 4 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 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 705 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KSO RELATED DB: PDB REMARK 900 RELATED ID: 5KSP RELATED DB: PDB REMARK 900 RELATED ID: 5KSY RELATED DB: PDB REMARK 900 RELATED ID: 5KSZ RELATED DB: PDB REMARK 900 RELATED ID: 5KU1 RELATED DB: PDB REMARK 900 RELATED ID: 5KUT RELATED DB: PDB DBREF 5KTY A 177 592 UNP Q8IXI2 MIRO1_HUMAN 177 592 SEQADV 5KTY LEU A 593 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY GLU A 594 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY HIS A 595 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY HIS A 596 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY HIS A 597 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY HIS A 598 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY HIS A 599 UNP Q8IXI2 EXPRESSION TAG SEQADV 5KTY HIS A 600 UNP Q8IXI2 EXPRESSION TAG SEQRES 1 A 424 GLU GLU LYS GLU MET LYS PRO ALA CYS ILE LYS ALA LEU SEQRES 2 A 424 THR ARG ILE PHE LYS ILE SER ASP GLN ASP ASN ASP GLY SEQRES 3 A 424 THR LEU ASN ASP ALA GLU LEU ASN PHE PHE GLN ARG ILE SEQRES 4 A 424 CYS PHE ASN THR PRO LEU ALA PRO GLN ALA LEU GLU ASP SEQRES 5 A 424 VAL LYS ASN VAL VAL ARG LYS HIS ILE SER ASP GLY VAL SEQRES 6 A 424 ALA ASP SER GLY LEU THR LEU LYS GLY PHE LEU PHE LEU SEQRES 7 A 424 HIS THR LEU PHE ILE GLN ARG GLY ARG HIS GLU THR THR SEQRES 8 A 424 TRP THR VAL LEU ARG ARG PHE GLY TYR ASP ASP ASP LEU SEQRES 9 A 424 ASP LEU THR PRO GLU TYR LEU PHE PRO LEU LEU LYS ILE SEQRES 10 A 424 PRO PRO ASP CYS THR THR GLU LEU ASN HIS HIS ALA TYR SEQRES 11 A 424 LEU PHE LEU GLN SER THR PHE ASP LYS HIS ASP LEU ASP SEQRES 12 A 424 ARG ASP CYS ALA LEU SER PRO ASP GLU LEU LYS ASP LEU SEQRES 13 A 424 PHE LYS VAL PHE PRO TYR ILE PRO TRP GLY PRO ASP VAL SEQRES 14 A 424 ASN ASN THR VAL CYS THR ASN GLU ARG GLY TRP ILE THR SEQRES 15 A 424 TYR GLN GLY PHE LEU SER GLN TRP THR LEU THR THR TYR SEQRES 16 A 424 LEU ASP VAL GLN ARG CYS LEU GLU TYR LEU GLY TYR LEU SEQRES 17 A 424 GLY TYR SER ILE LEU THR GLU GLN GLU SER GLN ALA SER SEQRES 18 A 424 ALA VAL THR VAL THR ARG ASP LYS LYS ILE ASP LEU GLN SEQRES 19 A 424 LYS LYS GLN THR GLN ARG ASN VAL PHE ARG CYS ASN VAL SEQRES 20 A 424 ILE GLY VAL LYS ASN CYS GLY LYS SER GLY VAL LEU GLN SEQRES 21 A 424 ALA LEU LEU GLY ARG ASN LEU MET ARG GLN LYS LYS ILE SEQRES 22 A 424 ARG GLU ASP HIS LYS SER TYR TYR ALA ILE ASN THR VAL SEQRES 23 A 424 TYR VAL TYR GLY GLN GLU LYS TYR LEU LEU LEU HIS ASP SEQRES 24 A 424 ILE SER GLU SER GLU PHE LEU THR GLU ALA GLU ILE ILE SEQRES 25 A 424 CYS ASP VAL VAL CYS LEU VAL TYR ASP VAL SER ASN PRO SEQRES 26 A 424 LYS SER PHE GLU TYR CYS ALA ARG ILE PHE LYS GLN HIS SEQRES 27 A 424 PHE MET ASP SER ARG ILE PRO CYS LEU ILE VAL ALA ALA SEQRES 28 A 424 LYS SER ASP LEU HIS GLU VAL LYS GLN GLU TYR SER ILE SEQRES 29 A 424 SER PRO THR ASP PHE CYS ARG LYS HIS LYS MET PRO PRO SEQRES 30 A 424 PRO GLN ALA PHE THR CYS ASN THR ALA ASP ALA PRO SER SEQRES 31 A 424 LYS ASP ILE PHE VAL LYS LEU THR THR MET ALA MET TYR SEQRES 32 A 424 PRO HIS VAL THR GLN ALA ASP LEU LYS SER SER THR PHE SEQRES 33 A 424 LEU GLU HIS HIS HIS HIS HIS HIS HET GDP A 701 28 HET MG A 702 1 HET GDP A 703 28 HET CA A 704 1 HET CA A 705 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM CA CALCIUM ION FORMUL 2 GDP 2(C10 H15 N5 O11 P2) FORMUL 3 MG MG 2+ FORMUL 5 CA 2(CA 2+) FORMUL 7 HOH *76(H2 O) HELIX 1 AA1 LYS A 182 ASP A 197 1 16 HELIX 2 AA2 ASN A 205 PHE A 217 1 13 HELIX 3 AA3 LEU A 226 ASN A 231 1 6 HELIX 4 AA4 THR A 247 ILE A 259 1 13 HELIX 5 AA5 THR A 266 PHE A 274 1 9 HELIX 6 AA6 THR A 283 PHE A 288 1 6 HELIX 7 AA7 ASN A 302 HIS A 316 1 15 HELIX 8 AA8 SER A 325 PHE A 333 1 9 HELIX 9 AA9 LYS A 334 PHE A 336 5 3 HELIX 10 AB1 ASP A 344 THR A 348 5 5 HELIX 11 AB2 TYR A 359 ASP A 373 1 15 HELIX 12 AB3 ASP A 373 LEU A 384 1 12 HELIX 13 AB4 GLY A 385 THR A 390 1 6 HELIX 14 AB5 SER A 394 SER A 397 5 4 HELIX 15 AB6 ASP A 404 LYS A 411 1 8 HELIX 16 AB7 GLY A 430 LEU A 439 1 10 HELIX 17 AB8 ASN A 442 LYS A 447 1 6 HELIX 18 AB9 GLU A 484 ILE A 488 5 5 HELIX 19 AC1 LYS A 502 PHE A 515 1 14 HELIX 20 AC2 SER A 541 HIS A 549 1 9 HELIX 21 AC3 LYS A 567 TYR A 579 1 13 SHEET 1 AA1 2 THR A 299 LEU A 301 0 SHEET 2 AA1 2 VAL A 399 VAL A 401 -1 O THR A 400 N GLU A 300 SHEET 1 AA2 2 ALA A 323 LEU A 324 0 SHEET 2 AA2 2 ILE A 357 THR A 358 -1 O ILE A 357 N LEU A 324 SHEET 1 AA3 6 TYR A 457 VAL A 464 0 SHEET 2 AA3 6 GLN A 467 ILE A 476 -1 O LYS A 469 N VAL A 462 SHEET 3 AA3 6 VAL A 418 ILE A 424 1 N CYS A 421 O LEU A 472 SHEET 4 AA3 6 VAL A 491 ASP A 497 1 O VAL A 495 N ILE A 424 SHEET 5 AA3 6 CYS A 522 ALA A 527 1 O LEU A 523 N VAL A 492 SHEET 6 AA3 6 GLN A 555 ALA A 556 1 O GLN A 555 N ILE A 524 LINK OD1 ASP A 197 CA CA A 704 1555 1555 2.19 LINK OD1 ASP A 199 CA CA A 704 1555 1555 2.18 LINK OD1 ASP A 201 CA CA A 704 1555 1555 2.21 LINK O THR A 203 CA CA A 704 1555 1555 2.24 LINK OE1 GLU A 208 CA CA A 704 1555 1555 2.28 LINK OE2 GLU A 208 CA CA A 704 1555 1555 2.63 LINK OD1 ASP A 317 CA CA A 705 1555 1555 2.21 LINK OD1 ASP A 319 CA CA A 705 1555 1555 2.18 LINK OD2 ASP A 319 CA CA A 705 1555 1555 3.20 LINK OD1 ASP A 321 CA CA A 705 1555 1555 2.25 LINK O ALA A 323 CA CA A 705 1555 1555 2.23 LINK OE1 GLU A 328 CA CA A 705 1555 1555 2.26 LINK OE2 GLU A 328 CA CA A 705 1555 1555 2.67 LINK OD1 ASN A 428 MG MG A 702 1555 1555 2.55 LINK O3B GDP A 701 MG MG A 702 1555 1555 2.34 LINK MG MG A 702 O3B GDP A 703 1555 1555 2.17 LINK MG MG A 702 O1A GDP A 703 1555 1555 2.09 LINK MG MG A 702 O HOH A 802 1555 1555 2.23 LINK CA CA A 704 O HOH A 829 1555 1555 2.15 LINK CA CA A 705 O HOH A 819 1555 1555 2.45 SITE 1 AC1 19 ASN A 428 CYS A 429 GLY A 430 LYS A 431 SITE 2 AC1 19 SER A 432 GLY A 433 LEU A 443 LYS A 447 SITE 3 AC1 19 LYS A 528 ASP A 530 LEU A 531 THR A 558 SITE 4 AC1 19 CYS A 559 ASN A 560 MG A 702 GDP A 703 SITE 5 AC1 19 HOH A 802 HOH A 818 HOH A 855 SITE 1 AC2 4 ASN A 428 GDP A 701 GDP A 703 HOH A 802 SITE 1 AC3 12 LYS A 427 ASN A 428 LYS A 431 LYS A 454 SITE 2 AC3 12 TYR A 456 ASP A 475 SER A 477 GLU A 478 SITE 3 AC3 12 GDP A 701 MG A 702 HOH A 802 HOH A 816 SITE 1 AC4 6 ASP A 197 ASP A 199 ASP A 201 THR A 203 SITE 2 AC4 6 GLU A 208 HOH A 829 SITE 1 AC5 6 ASP A 317 ASP A 319 ASP A 321 ALA A 323 SITE 2 AC5 6 GLU A 328 HOH A 819 CRYST1 74.073 74.073 222.175 90.00 90.00 90.00 P 43 21 2 8 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 0.013500 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013500 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004501 0.00000