HEADER ISOMERASE 12-JAN-10 2X2A TITLE FREE ACETYL-CYPA TRIGONAL FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PPIASE A, ROTAMASE A, CYCLOPHILIN A, CYCLOSPORIN COMPND 5 A-BINDING PROTEIN, CYPA; COMPND 6 EC: 5.2.1.8 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS HIV-1, ISOMERASE, HOST-VIRUS INTERACTION EXPDTA X-RAY DIFFRACTION AUTHOR M.LAMMERS,H.NEUMANN,J.W.CHIN,L.C.JAMES REVDAT 2 15-JUN-11 2X2A 1 JRNL REMARK HETSYN REVDAT 1 23-MAR-10 2X2A 0 JRNL AUTH M.LAMMERS,H.NEUMANN,J.W.CHIN,L.C.JAMES JRNL TITL ACETYLATION REGULATES CYCLOPHILIN A CATALYSIS, JRNL TITL 2 IMMUNOSUPPRESSION AND HIV ISOMERIZATION. JRNL REF NAT.CHEM.BIOL. V. 6 331 2010 JRNL REFN ISSN 1552-4450 JRNL PMID 20364129 JRNL DOI 10.1038/NCHEMBIO.342 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.95 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.63 REMARK 3 NUMBER OF REFLECTIONS : 78594 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) : 0.12511 REMARK 3 R VALUE (WORKING SET) : 0.12324 REMARK 3 FREE R VALUE : 0.16123 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 4141 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) : 1.400 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.436 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5792 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.97 REMARK 3 BIN R VALUE (WORKING SET) : 0.198 REMARK 3 BIN FREE R VALUE SET COUNT : 278 REMARK 3 BIN FREE R VALUE : 0.261 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2504 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 586 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.132 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.51 REMARK 3 B22 (A**2) : 0.51 REMARK 3 B33 (A**2) : -0.77 REMARK 3 B12 (A**2) : 0.26 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.044 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.046 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.026 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.477 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2593 ; 0.027 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1826 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3467 ; 2.104 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4401 ; 1.122 ; 3.002 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 323 ; 6.069 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;33.008 ;24.138 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 439 ;12.191 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.824 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.142 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2893 ; 0.011 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 553 ; 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): 1605 ; 2.596 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 690 ; 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2554 ; 3.561 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 988 ; 5.073 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 913 ; 6.845 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 4419 ; 2.636 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 586 ;13.511 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 4370 ; 6.725 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : B A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 1 B 180 6 REMARK 3 1 A 1 A 180 6 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 LOOSE POSITIONAL 1 A (A): 2167 ; 0.48 ; 5.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 2167 ; 3.72 ; 10.00 REMARK 3 LOOSE POSITIONAL 1 B (A): 2167 ; 0.48 ; 5.00 REMARK 3 LOOSE THERMAL 1 B (A**2): 2167 ; 3.72 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES REFINED INDIVIDUALLY. REMARK 3 HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 4 REMARK 4 2X2A COMPLIES WITH FORMAT V. 3.20, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-10. REMARK 100 THE PDBE ID CODE IS EBI-42417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 287 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 83025 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.40 REMARK 200 RESOLUTION RANGE LOW (A) : 27.80 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 6.9 REMARK 200 R MERGE (I) : 0.10 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.20 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL 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 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 115.93333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.96667 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.96667 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 115.93333 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.7 KCAL/MOL 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 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 MET B 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 N MET A 1 O HOH A 2002 2.17 REMARK 500 N MET A 1 O HOH A 2003 2.05 REMARK 500 CA MET A 1 O HOH A 2004 2.13 REMARK 500 C MET A 1 O HOH A 2004 2.15 REMARK 500 CG2 VAL A 29 O HOH A 2060 1.75 REMARK 500 O PHE A 53 O HOH A 2117 2.08 REMARK 500 NE ARG A 55 O HOH A 2123 1.90 REMARK 500 NH2 ARG A 55 O HOH A 2123 2.17 REMARK 500 CG MET A 61 O HOH A 2133 1.62 REMARK 500 SD MET A 61 O HOH A 2133 1.78 REMARK 500 CE MET A 61 O HOH A 2133 2.12 REMARK 500 SG CYS A 115 O HOH A 2219 1.93 REMARK 500 O LYS A 151 O HOH A 2261 2.14 REMARK 500 NE2 GLN A 163 O HOH A 2285 1.99 REMARK 500 NZ LYS B 120 O HOH B 2217 1.40 REMARK 500 NE2 GLN B 163 O HOH B 2282 1.99 REMARK 500 O2 SO4 B 1166 O HOH B 2287 2.17 REMARK 500 O HOH A 2003 O HOH A 2004 1.51 REMARK 500 O HOH A 2007 O HOH A 2010 2.07 REMARK 500 O HOH A 2008 O HOH A 2009 1.67 REMARK 500 O HOH A 2016 O HOH A 2031 0.89 REMARK 500 O HOH A 2029 O HOH A 2272 2.12 REMARK 500 O HOH A 2047 O HOH A 2121 2.18 REMARK 500 O HOH A 2063 O HOH A 2156 2.07 REMARK 500 O HOH A 2067 O HOH A 2068 0.61 REMARK 500 O HOH A 2069 O HOH A 2070 0.55 REMARK 500 O HOH A 2071 O HOH B 2149 1.59 REMARK 500 O HOH A 2071 O HOH A 2168 2.14 REMARK 500 O HOH A 2078 O HOH A 2191 2.07 REMARK 500 O HOH A 2081 O HOH A 2211 2.19 REMARK 500 O HOH A 2116 O HOH A 2117 0.78 REMARK 500 O HOH A 2120 O HOH A 2121 2.02 REMARK 500 O HOH A 2120 O HOH A 2264 1.69 REMARK 500 O HOH A 2123 O HOH B 2201 1.37 REMARK 500 O HOH A 2124 O HOH B 2202 1.98 REMARK 500 O HOH A 2125 O HOH A 2254 1.80 REMARK 500 O HOH A 2155 O HOH A 2156 1.19 REMARK 500 O HOH A 2161 O HOH A 2166 2.06 REMARK 500 O HOH A 2162 O HOH A 2207 1.95 REMARK 500 O HOH A 2176 O HOH A 2231 1.02 REMARK 500 O HOH A 2186 O HOH A 2187 1.02 REMARK 500 O HOH A 2195 O HOH A 2208 1.00 REMARK 500 O HOH A 2196 O HOH A 2209 0.50 REMARK 500 O HOH A 2197 O HOH A 2199 1.80 REMARK 500 O HOH A 2201 O HOH A 2202 1.87 REMARK 500 O HOH A 2210 O HOH A 2211 1.12 REMARK 500 O HOH A 2224 O HOH A 2230 0.65 REMARK 500 O HOH A 2251 O HOH A 2252 0.88 REMARK 500 O HOH A 2254 O HOH A 2268 2.15 REMARK 500 O HOH A 2259 O HOH A 2260 2.20 REMARK 500 REMARK 500 THIS ENTRY HAS 77 CLOSE CONTACTS REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 2161 O HOH A 2250 4545 1.85 REMARK 500 O HOH B 2039 O HOH A 2244 2544 1.47 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 VAL A 29 CB VAL A 29 CG2 -0.154 REMARK 500 CYS A 115 CB CYS A 115 SG -0.118 REMARK 500 VAL B 6 CB VAL B 6 CG2 -0.167 REMARK 500 GLU B 15 CD GLU B 15 OE1 0.109 REMARK 500 GLU B 81 CB GLU B 81 CG 0.117 REMARK 500 GLU B 81 CG GLU B 81 CD 0.101 REMARK 500 LYS B 120 CD LYS B 120 CE 0.246 REMARK 500 LYS B 120 CG LYS B 120 CD 0.311 REMARK 500 ALY B 125 C HIS B 126 N 0.148 REMARK 500 GLU B 134 CD GLU B 134 OE1 0.071 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 MET A 1 CG - SD - CE ANGL. DEV. = -16.7 DEGREES REMARK 500 VAL A 2 CA - CB - CG1 ANGL. DEV. = 9.0 DEGREES REMARK 500 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 ARG A 69 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP B 13 CB - CG - OD2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG B 55 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 LYS B 120 CD - CE - NZ ANGL. DEV. = 16.1 DEGREES REMARK 500 LYS B 120 CG - CD - CE ANGL. DEV. = -31.5 DEGREES REMARK 500 ARG B 148 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES 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 60 -68.59 -124.88 REMARK 500 THR A 119 67.20 -119.45 REMARK 500 PHE B 60 -79.51 -130.57 REMARK 500 PHE B 129 -1.49 -143.37 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 GOL A1166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A1167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1166 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1VBS RELATED DB: PDB REMARK 900 STRUCTURE OF CYCLOPHILIN COMPLEXED WITH (D) REMARK 900 ALA CONTAINING TETRAPEPTIDE REMARK 900 RELATED ID: 1OCA RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A, UNLIGATED, NMR, 20 REMARK 900 STRUCTURES REMARK 900 RELATED ID: 1MF8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CALCINEURIN REMARK 900 COMPLEXED WITHCYCLOSPORIN A AND HUMAN REMARK 900 CYCLOPHILIN REMARK 900 RELATED ID: 2CYH RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE ALA-PRO REMARK 900 RELATED ID: 1CWB RELATED DB: PDB REMARK 900 RELATED ID: 1VBT RELATED DB: PDB REMARK 900 STRUCTURE OF CYCLOPHILIN COMPLEXED WITH SULFUR REMARK 900 -SUBSTITUTED TETRAPEPTIDE AAPF REMARK 900 RELATED ID: 1M9E RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/ REMARK 900 HIV-1 CA N-TERMINAL DOMAIN (1-146) M- REMARK 900 TYPE H87A COMPLEX. REMARK 900 RELATED ID: 1CWL RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 4 4- REMARK 900 HYDROXY-MELEU CYCLOSPORIN REMARK 900 RELATED ID: 1CWC RELATED DB: PDB REMARK 900 RELATED ID: 1CWO RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH THR2, REMARK 900 LEU5, D-HIV8, LEU10 CYCLOSPORIN REMARK 900 RELATED ID: 1CWI RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 2-VAL 3 REMARK 900 -(N-METHYL)-D-ALANINE CYCLOSPORIN REMARK 900 RELATED ID: 1RMH RELATED DB: PDB REMARK 900 RECOMBINANT CYCLOPHILIN A FROM HUMAN T CELL REMARK 900 RELATED ID: 1CWJ RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 2-VAL 3 REMARK 900 -S-METHYL-SARCOSINE CYCLOSPORIN REMARK 900 RELATED ID: 2RMB RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH DIMETHYL- REMARK 900 CYCLOSPORIN A REMARK 900 RELATED ID: 1M9C RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/ REMARK 900 HIV-1 CA N-TERMINAL DOMAIN (1-146) M- REMARK 900 TYPE COMPLEX. REMARK 900 RELATED ID: 1CWA RELATED DB: PDB REMARK 900 RELATED ID: 1CWF RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 2-VAL REMARK 900 CYCLOSPORIN REMARK 900 RELATED ID: 3CYH RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE SER-PRO REMARK 900 RELATED ID: 1M9Y RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/ REMARK 900 HIV-1 CA N-TERMINAL DOMAIN (1-146) M- REMARK 900 TYPE H87A,G89A COMPLEX. REMARK 900 RELATED ID: 4CYH RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE HIS-PRO REMARK 900 RELATED ID: 1M9F RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/ REMARK 900 HIV-1 CA N-TERMINAL DOMAIN (1-146) M- REMARK 900 TYPE H87A,A88M COMPLEX. REMARK 900 RELATED ID: 1CWH RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 3-D-SER REMARK 900 CYCLOSPORIN REMARK 900 RELATED ID: 1BCK RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 2-THR REMARK 900 CYCLOSPORIN REMARK 900 RELATED ID: 1W8V RELATED DB: PDB REMARK 900 ENZYMATIC AND STRUCTURAL CHARACTERIZATION OF REMARK 900 NON PEPTIDE LIGAND CYCLOPHILIN COMPLEXES REMARK 900 RELATED ID: 1AWR RELATED DB: PDB REMARK 900 CYPA COMPLEXED WITH HAGPIA REMARK 900 RELATED ID: 1NMK RELATED DB: PDB REMARK 900 THE SANGLIFEHRIN-CYCLOPHILIN INTERACTION: REMARK 900 DEGRADATION WORK,SYNTHETIC MACROCYCLIC ANALOGUES REMARK 900 , X-RAY CRYSTAL STRUCTUREAND BINDING DATA REMARK 900 RELATED ID: 1MIK RELATED DB: PDB REMARK 900 RELATED ID: 1AWV RELATED DB: PDB REMARK 900 CYPA COMPLEXED WITH HVGPIA REMARK 900 RELATED ID: 1M9D RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/ REMARK 900 HIV-1 CA N-TERMINAL DOMAIN (1-146) O- REMARK 900 TYPE CHIMERA COMPLEX. REMARK 900 RELATED ID: 1AWT RELATED DB: PDB REMARK 900 SECYPA COMPLEXED WITH HAGPIA REMARK 900 RELATED ID: 1FGL RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH A FRAGMENT OF REMARK 900 HIV-1 GAGPROTEIN REMARK 900 RELATED ID: 2CPL RELATED DB: PDB REMARK 900 CYCLOPHILIN A REMARK 900 RELATED ID: 1M9X RELATED DB: PDB REMARK 900 X-RAY CRYSTAL STRUCTURE OF CYCLOPHILIN A/ REMARK 900 HIV-1 CA N-TERMINAL DOMAIN (1-146) M- REMARK 900 TYPE H87A,A88M,G89A COMPLEX. REMARK 900 RELATED ID: 1CWK RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 1-(6,7 REMARK 900 -DIHYDRO)MEBMT 2-VAL 3-D-(2-S-METHYL) REMARK 900 SARCOSINE CYCLOSPORIN REMARK 900 RELATED ID: 1M63 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CALCINEURIN-CYCLOPHILIN- REMARK 900 CYCLOSPORINSHOWS COMMON BUT DISTINCT RECOGNITION REMARK 900 OF IMMUNOPHILIN-DRUGCOMPLEXES REMARK 900 RELATED ID: 5CYH RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH DIPEPTIDE GLY-PRO REMARK 900 RELATED ID: 1AK4 RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A BOUND TO THE AMINO- REMARK 900 TERMINAL DOMAIN OF HIV-1 CAPSID REMARK 900 RELATED ID: 3CYS RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A REMARK 900 (NMR, 22 STRUCTURES) REMARK 900 RELATED ID: 1W8L RELATED DB: PDB REMARK 900 ENZYMATIC AND STRUCTURAL CHARACTERIZATION OF REMARK 900 NON PEPTIDE LIGAND CYCLOPHILIN COMPLEXES REMARK 900 RELATED ID: 2ALF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN CYPA MUTANT K131A REMARK 900 RELATED ID: 1AWS RELATED DB: PDB REMARK 900 SECYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC REMARK 900 MONOMER) REMARK 900 RELATED ID: 2X25 RELATED DB: PDB REMARK 900 FREE ACETYL-CYPA ORTHOROMBIC FORM REMARK 900 RELATED ID: 1W8M RELATED DB: PDB REMARK 900 ENZYMATIC AND STRUCTURAL CHARACTERISATION OF REMARK 900 NON PEPTIDE LIGAND CYCLOPHILIN COMPLEXES REMARK 900 RELATED ID: 1AWU RELATED DB: PDB REMARK 900 CYPA COMPLEXED WITH HVGPIA (PSEUDO-SYMMETRIC REMARK 900 MONOMER) REMARK 900 RELATED ID: 2RMA RELATED DB: PDB REMARK 900 CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A REMARK 900 RELATED ID: 1CWM RELATED DB: PDB REMARK 900 HUMAN CYCLOPHILIN A COMPLEXED WITH 4 MEILE REMARK 900 CYCLOSPORIN REMARK 900 RELATED ID: 1AWQ RELATED DB: PDB REMARK 900 CYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC REMARK 900 MONOMER) REMARK 900 RELATED ID: 2X2D RELATED DB: PDB REMARK 900 ACETYL-CYPA:HIV-1 N-TERM CAPSID DOMAIN REMARK 900 COMPLEX REMARK 900 RELATED ID: 2X2C RELATED DB: PDB REMARK 900 ACETYL-CYPA:CYCLOSPORINE COMPLEX DBREF 2X2A A 1 165 UNP P62937 PPIA_HUMAN 1 165 DBREF 2X2A B 1 165 UNP P62937 PPIA_HUMAN 1 165 SEQADV 2X2A LYS A 120 UNP P62937 GLU 120 CONFLICT SEQADV 2X2A LYS B 120 UNP P62937 GLU 120 CONFLICT SEQRES 1 A 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP SEQRES 2 A 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA SEQRES 3 A 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 A 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS SEQRES 5 A 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY SEQRES 6 A 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 A 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS SEQRES 8 A 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY SEQRES 9 A 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA SEQRES 10 A 165 LYS THR LYS TRP LEU ASP GLY ALY HIS VAL VAL PHE GLY SEQRES 11 A 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU SEQRES 12 A 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE SEQRES 13 A 165 THR ILE ALA ASP CYS GLY GLN LEU GLU SEQRES 1 B 165 MET VAL ASN PRO THR VAL PHE PHE ASP ILE ALA VAL ASP SEQRES 2 B 165 GLY GLU PRO LEU GLY ARG VAL SER PHE GLU LEU PHE ALA SEQRES 3 B 165 ASP LYS VAL PRO LYS THR ALA GLU ASN PHE ARG ALA LEU SEQRES 4 B 165 SER THR GLY GLU LYS GLY PHE GLY TYR LYS GLY SER CYS SEQRES 5 B 165 PHE HIS ARG ILE ILE PRO GLY PHE MET CYS GLN GLY GLY SEQRES 6 B 165 ASP PHE THR ARG HIS ASN GLY THR GLY GLY LYS SER ILE SEQRES 7 B 165 TYR GLY GLU LYS PHE GLU ASP GLU ASN PHE ILE LEU LYS SEQRES 8 B 165 HIS THR GLY PRO GLY ILE LEU SER MET ALA ASN ALA GLY SEQRES 9 B 165 PRO ASN THR ASN GLY SER GLN PHE PHE ILE CYS THR ALA SEQRES 10 B 165 LYS THR LYS TRP LEU ASP GLY ALY HIS VAL VAL PHE GLY SEQRES 11 B 165 LYS VAL LYS GLU GLY MET ASN ILE VAL GLU ALA MET GLU SEQRES 12 B 165 ARG PHE GLY SER ARG ASN GLY LYS THR SER LYS LYS ILE SEQRES 13 B 165 THR ILE ALA ASP CYS GLY GLN LEU GLU MODRES 2X2A ALY A 125 LYS N(6)-ACETYLLYSINE MODRES 2X2A ALY B 125 LYS N(6)-ACETYLLYSINE HET ALY A 125 12 HET ALY B 125 12 HET GOL A1166 6 HET SO4 A1167 5 HET SO4 B1166 5 HETNAM ALY N(6)-ACETYLLYSINE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN FORMUL 3 ALY 2(C8 H16 N2 O3) FORMUL 4 GOL C3 H8 O3 FORMUL 5 SO4 2(O4 S 2-) FORMUL 6 HOH *586(H2 O) HELIX 1 1 VAL A 29 GLY A 42 1 14 HELIX 2 2 THR A 119 ASP A 123 5 5 HELIX 3 3 GLY A 135 ARG A 144 1 10 HELIX 4 4 VAL B 29 GLY B 42 1 14 HELIX 5 5 THR B 119 ASP B 123 5 5 HELIX 6 6 GLY B 135 ARG B 144 1 10 SHEET 1 AA 8 ARG A 55 ILE A 57 0 SHEET 2 AA 8 MET A 61 GLY A 64 -1 O MET A 61 N ILE A 57 SHEET 3 AA 8 PHE A 112 CYS A 115 -1 O PHE A 112 N GLY A 64 SHEET 4 AA 8 ILE A 97 MET A 100 -1 O ILE A 97 N CYS A 115 SHEET 5 AA 8 VAL A 128 GLU A 134 -1 N PHE A 129 O LEU A 98 SHEET 6 AA 8 GLU A 15 LEU A 24 -1 O SER A 21 N LYS A 133 SHEET 7 AA 8 THR A 5 VAL A 12 -1 O VAL A 6 N PHE A 22 SHEET 8 AA 8 ILE A 156 GLN A 163 -1 O THR A 157 N ALA A 11 SHEET 1 BA 8 ARG B 55 ILE B 57 0 SHEET 2 BA 8 MET B 61 GLY B 64 -1 O MET B 61 N ILE B 57 SHEET 3 BA 8 PHE B 112 CYS B 115 -1 O PHE B 112 N GLY B 64 SHEET 4 BA 8 ILE B 97 MET B 100 -1 O ILE B 97 N CYS B 115 SHEET 5 BA 8 VAL B 128 GLU B 134 -1 N PHE B 129 O LEU B 98 SHEET 6 BA 8 GLU B 15 LEU B 24 -1 O SER B 21 N LYS B 133 SHEET 7 BA 8 THR B 5 VAL B 12 -1 O VAL B 6 N PHE B 22 SHEET 8 BA 8 ILE B 156 LEU B 164 -1 O THR B 157 N ALA B 11 LINK C GLY A 124 N ALY A 125 1555 1555 1.37 LINK C ALY A 125 N HIS A 126 1555 1555 1.36 LINK C GLY B 124 N ALY B 125 1555 1555 1.36 LINK C ALY B 125 N HIS B 126 1555 1555 1.47 SITE 1 AC1 8 ARG A 37 GLU A 43 TRP A 121 HOH A2073 SITE 2 AC1 8 HOH A2095 HOH A2292 HOH A2293 TRP B 121 SITE 1 AC2 7 ARG A 148 ASN A 149 HOH A2294 HOH A2295 SITE 2 AC2 7 HOH A2296 HOH A2297 HOH A2298 SITE 1 AC3 5 SER B 147 ARG B 148 HOH B2286 HOH B2287 SITE 2 AC3 5 HOH B2288 CRYST1 64.300 64.300 173.900 90.00 90.00 120.00 P 32 2 1 12 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 0.015552 0.008979 0.000000 0.00000 SCALE2 0.000000 0.017958 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005750 0.00000