HEADER PROTEIN TRANSPORT 30-OCT-23 8R02 TITLE CRYSTAL STRUCTURE OF THE RETROMER COMPLEX VPS29/VPS35 WITH THE LIGAND TITLE 2 BIS-1,3-PHENYL GUANYLHYDRAZONE, 2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 29; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 35; COMPND 7 CHAIN: C, D; 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: VPS29; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: VPS35; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, TRANSPORT, RECYCLING, LIGAND, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.MILANI,E.FAGNANI REVDAT 1 27-MAR-24 8R02 0 JRNL AUTH E.FAGNANI,F.BONI,P.SENECI,D.GORNATI,L.MUZIO,E.MASTRANGELO, JRNL AUTH 2 M.MILANI JRNL TITL STABILIZATION OF THE RETROMER COMPLEX: ANALYSIS OF NOVEL JRNL TITL 2 BINDING SITES OF BIS-1,3-PHENYL GUANYLHYDRAZONE 2A TO THE JRNL TITL 3 VPS29/VPS35 INTERFACE. JRNL REF COMPUT STRUCT BIOTECHNOL J V. 23 1088 2024 JRNL REFN ESSN 2001-0370 JRNL PMID 38487369 JRNL DOI 10.1016/J.CSBJ.2024.02.026 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 40436 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.264 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.998 REMARK 3 FREE R VALUE TEST SET COUNT : 2021 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2716 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.4170 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.3970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7729 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 64 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 115.5 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.56500 REMARK 3 B22 (A**2) : -3.07400 REMARK 3 B33 (A**2) : -2.49100 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.537 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.303 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.323 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 33.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7914 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 7567 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10691 ; 1.444 ; 1.839 REMARK 3 BOND ANGLES OTHERS (DEGREES): 17431 ; 0.804 ; 1.771 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 960 ; 5.848 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 39 ;18.753 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1425 ;17.184 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1183 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 9209 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1821 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1694 ; 0.224 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 46 ; 0.336 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3822 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 137 ; 0.140 ; 0.200 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): 3846 ; 6.839 ; 9.556 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3846 ; 6.839 ; 9.556 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4801 ; 9.957 ;17.173 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4802 ; 9.956 ;17.173 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4068 ; 7.041 ;10.263 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 4069 ; 7.041 ;10.262 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5889 ;10.748 ;18.606 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5890 ;10.747 ;18.605 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 182 NULL REMARK 3 1 A 1 A 182 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : A REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 2 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 2 A 489 A 778 NULL REMARK 3 2 A 489 A 778 NULL REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 182 REMARK 3 ORIGIN FOR THE GROUP (A): -11.4609 1.5870 1.0646 REMARK 3 T TENSOR REMARK 3 T11: 0.2034 T22: 0.1518 REMARK 3 T33: 0.0965 T12: 0.0468 REMARK 3 T13: 0.1087 T23: 0.0050 REMARK 3 L TENSOR REMARK 3 L11: 0.2254 L22: 2.1213 REMARK 3 L33: 0.6608 L12: 0.1076 REMARK 3 L13: -0.0140 L23: -0.0371 REMARK 3 S TENSOR REMARK 3 S11: -0.0259 S12: 0.1223 S13: -0.0785 REMARK 3 S21: 0.4719 S22: 0.0285 S23: 0.2129 REMARK 3 S31: -0.1403 S32: -0.1173 S33: -0.0025 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -12.5500 -44.3099 -16.2045 REMARK 3 T TENSOR REMARK 3 T11: 0.4101 T22: 0.1607 REMARK 3 T33: 0.1621 T12: 0.0463 REMARK 3 T13: -0.2041 T23: 0.0082 REMARK 3 L TENSOR REMARK 3 L11: 0.1214 L22: 3.5154 REMARK 3 L33: 0.6646 L12: 0.1176 REMARK 3 L13: 0.1835 L23: 1.1082 REMARK 3 S TENSOR REMARK 3 S11: -0.0210 S12: 0.0136 S13: 0.0791 REMARK 3 S21: 1.0937 S22: 0.1065 S23: -0.4340 REMARK 3 S31: 0.3330 S32: -0.0787 S33: -0.0855 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): 3.0702 8.4066 -12.6731 REMARK 3 T TENSOR REMARK 3 T11: 0.1879 T22: 0.1276 REMARK 3 T33: 0.0821 T12: 0.0242 REMARK 3 T13: -0.0169 T23: 0.0762 REMARK 3 L TENSOR REMARK 3 L11: 0.0804 L22: 0.9548 REMARK 3 L33: 0.9759 L12: 0.0878 REMARK 3 L13: -0.2141 L23: -0.7051 REMARK 3 S TENSOR REMARK 3 S11: 0.0646 S12: 0.0450 S13: -0.0031 REMARK 3 S21: -0.0658 S22: -0.2004 S23: -0.1717 REMARK 3 S31: -0.2328 S32: 0.0808 S33: 0.1358 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -23.3645 -45.8542 -34.3822 REMARK 3 T TENSOR REMARK 3 T11: 0.0736 T22: 0.0668 REMARK 3 T33: 0.1111 T12: 0.0447 REMARK 3 T13: -0.0259 T23: -0.0453 REMARK 3 L TENSOR REMARK 3 L11: 0.0667 L22: 3.1980 REMARK 3 L33: 0.8809 L12: 0.2228 REMARK 3 L13: 0.2306 L23: 1.0292 REMARK 3 S TENSOR REMARK 3 S11: -0.0235 S12: -0.0030 S13: 0.0399 REMARK 3 S21: -0.1886 S22: -0.0652 S23: 0.2000 REMARK 3 S31: 0.0041 S32: 0.0278 S33: 0.0887 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8R02 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1292134345. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91788 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40494 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.919 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.60 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 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) : 2.55 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 150 MM NAK TARTRATE, 100 REMARK 280 MM NACL, PH 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 SMTRY1 2 -1.000000 0.000000 0.000000 28.75000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.67000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 70.41500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 70.67000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.75000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 70.41500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 MET A -2 REMARK 465 GLU A -1 REMARK 465 HIS A 0 REMARK 465 MET B -2 REMARK 465 GLU B -1 REMARK 465 HIS B 0 REMARK 465 ARG C 780 REMARK 465 MET D 475 REMARK 465 VAL D 476 REMARK 465 GLU D 477 REMARK 465 ASP D 478 REMARK 465 PRO D 479 REMARK 465 ASP D 480 REMARK 465 PRO D 481 REMARK 465 GLU D 482 REMARK 465 ASP D 483 REMARK 465 PHE D 484 REMARK 465 ALA D 485 REMARK 465 ASP D 486 REMARK 465 GLU D 487 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU C 779 CG CD1 CD2 REMARK 470 GLN D 488 CG CD OE1 NE2 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 CYS A 41 -11.28 79.43 REMARK 500 HIS A 115 -45.47 74.92 REMARK 500 GLU A 125 51.78 34.58 REMARK 500 TYR A 139 150.06 -47.12 REMARK 500 SER A 158 15.89 48.22 REMARK 500 ASN B 39 32.57 72.15 REMARK 500 CYS B 41 -38.23 84.45 REMARK 500 HIS B 115 -43.93 75.91 REMARK 500 GLU B 125 54.44 34.66 REMARK 500 GLN B 156 -95.70 -116.23 REMARK 500 GLU C 575 35.17 73.47 REMARK 500 ALA C 577 -53.49 -131.10 REMARK 500 ASN C 598 13.88 86.38 REMARK 500 TRP C 678 -66.81 -108.08 REMARK 500 MET C 711 -53.49 81.13 REMARK 500 SER D 489 -71.34 -160.29 REMARK 500 LEU D 490 58.12 -106.93 REMARK 500 GLU D 575 35.75 73.87 REMARK 500 ALA D 577 -54.80 -129.40 REMARK 500 ASN D 598 14.93 84.75 REMARK 500 TRP D 678 -67.65 -107.74 REMARK 500 MET D 711 -58.61 80.24 REMARK 500 ARG D 778 49.45 70.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG C 726 0.25 SIDE CHAIN REMARK 500 ARG D 493 0.23 SIDE CHAIN REMARK 500 ARG D 681 0.29 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 8R02 A 1 182 UNP Q9UBQ0 VPS29_HUMAN 1 182 DBREF 8R02 B 1 182 UNP Q9UBQ0 VPS29_HUMAN 1 182 DBREF 8R02 C 476 780 UNP Q96QK1 VPS35_HUMAN 476 780 DBREF 8R02 D 476 780 UNP Q96QK1 VPS35_HUMAN 476 780 SEQADV 8R02 MET A -2 UNP Q9UBQ0 INITIATING METHIONINE SEQADV 8R02 GLU A -1 UNP Q9UBQ0 EXPRESSION TAG SEQADV 8R02 HIS A 0 UNP Q9UBQ0 EXPRESSION TAG SEQADV 8R02 MET B -2 UNP Q9UBQ0 INITIATING METHIONINE SEQADV 8R02 GLU B -1 UNP Q9UBQ0 EXPRESSION TAG SEQADV 8R02 HIS B 0 UNP Q9UBQ0 EXPRESSION TAG SEQADV 8R02 MET C 475 UNP Q96QK1 INITIATING METHIONINE SEQADV 8R02 MET D 475 UNP Q96QK1 INITIATING METHIONINE SEQRES 1 A 185 MET GLU HIS MET LEU VAL LEU VAL LEU GLY ASP LEU HIS SEQRES 2 A 185 ILE PRO HIS ARG CYS ASN SER LEU PRO ALA LYS PHE LYS SEQRES 3 A 185 LYS LEU LEU VAL PRO GLY LYS ILE GLN HIS ILE LEU CYS SEQRES 4 A 185 THR GLY ASN LEU CYS THR LYS GLU SER TYR ASP TYR LEU SEQRES 5 A 185 LYS THR LEU ALA GLY ASP VAL HIS ILE VAL ARG GLY ASP SEQRES 6 A 185 PHE ASP GLU ASN LEU ASN TYR PRO GLU GLN LYS VAL VAL SEQRES 7 A 185 THR VAL GLY GLN PHE LYS ILE GLY LEU ILE HIS GLY HIS SEQRES 8 A 185 GLN VAL ILE PRO TRP GLY ASP MET ALA SER LEU ALA LEU SEQRES 9 A 185 LEU GLN ARG GLN PHE ASP VAL ASP ILE LEU ILE SER GLY SEQRES 10 A 185 HIS THR HIS LYS PHE GLU ALA PHE GLU HIS GLU ASN LYS SEQRES 11 A 185 PHE TYR ILE ASN PRO GLY SER ALA THR GLY ALA TYR ASN SEQRES 12 A 185 ALA LEU GLU THR ASN ILE ILE PRO SER PHE VAL LEU MET SEQRES 13 A 185 ASP ILE GLN ALA SER THR VAL VAL THR TYR VAL TYR GLN SEQRES 14 A 185 LEU ILE GLY ASP ASP VAL LYS VAL GLU ARG ILE GLU TYR SEQRES 15 A 185 LYS LYS PRO SEQRES 1 B 185 MET GLU HIS MET LEU VAL LEU VAL LEU GLY ASP LEU HIS SEQRES 2 B 185 ILE PRO HIS ARG CYS ASN SER LEU PRO ALA LYS PHE LYS SEQRES 3 B 185 LYS LEU LEU VAL PRO GLY LYS ILE GLN HIS ILE LEU CYS SEQRES 4 B 185 THR GLY ASN LEU CYS THR LYS GLU SER TYR ASP TYR LEU SEQRES 5 B 185 LYS THR LEU ALA GLY ASP VAL HIS ILE VAL ARG GLY ASP SEQRES 6 B 185 PHE ASP GLU ASN LEU ASN TYR PRO GLU GLN LYS VAL VAL SEQRES 7 B 185 THR VAL GLY GLN PHE LYS ILE GLY LEU ILE HIS GLY HIS SEQRES 8 B 185 GLN VAL ILE PRO TRP GLY ASP MET ALA SER LEU ALA LEU SEQRES 9 B 185 LEU GLN ARG GLN PHE ASP VAL ASP ILE LEU ILE SER GLY SEQRES 10 B 185 HIS THR HIS LYS PHE GLU ALA PHE GLU HIS GLU ASN LYS SEQRES 11 B 185 PHE TYR ILE ASN PRO GLY SER ALA THR GLY ALA TYR ASN SEQRES 12 B 185 ALA LEU GLU THR ASN ILE ILE PRO SER PHE VAL LEU MET SEQRES 13 B 185 ASP ILE GLN ALA SER THR VAL VAL THR TYR VAL TYR GLN SEQRES 14 B 185 LEU ILE GLY ASP ASP VAL LYS VAL GLU ARG ILE GLU TYR SEQRES 15 B 185 LYS LYS PRO SEQRES 1 C 306 MET VAL GLU ASP PRO ASP PRO GLU ASP PHE ALA ASP GLU SEQRES 2 C 306 GLN SER LEU VAL GLY ARG PHE ILE HIS LEU LEU ARG SER SEQRES 3 C 306 GLU ASP PRO ASP GLN GLN TYR LEU ILE LEU ASN THR ALA SEQRES 4 C 306 ARG LYS HIS PHE GLY ALA GLY GLY ASN GLN ARG ILE ARG SEQRES 5 C 306 PHE THR LEU PRO PRO LEU VAL PHE ALA ALA TYR GLN LEU SEQRES 6 C 306 ALA PHE ARG TYR LYS GLU ASN SER LYS VAL ASP ASP LYS SEQRES 7 C 306 TRP GLU LYS LYS CYS GLN LYS ILE PHE SER PHE ALA HIS SEQRES 8 C 306 GLN THR ILE SER ALA LEU ILE LYS ALA GLU LEU ALA GLU SEQRES 9 C 306 LEU PRO LEU ARG LEU PHE LEU GLN GLY ALA LEU ALA ALA SEQRES 10 C 306 GLY GLU ILE GLY PHE GLU ASN HIS GLU THR VAL ALA TYR SEQRES 11 C 306 GLU PHE MET SER GLN ALA PHE SER LEU TYR GLU ASP GLU SEQRES 12 C 306 ILE SER ASP SER LYS ALA GLN LEU ALA ALA ILE THR LEU SEQRES 13 C 306 ILE ILE GLY THR PHE GLU ARG MET LYS CYS PHE SER GLU SEQRES 14 C 306 GLU ASN HIS GLU PRO LEU ARG THR GLN CYS ALA LEU ALA SEQRES 15 C 306 ALA SER LYS LEU LEU LYS LYS PRO ASP GLN GLY ARG ALA SEQRES 16 C 306 VAL SER THR CYS ALA HIS LEU PHE TRP SER GLY ARG ASN SEQRES 17 C 306 THR ASP LYS ASN GLY GLU GLU LEU HIS GLY GLY LYS ARG SEQRES 18 C 306 VAL MET GLU CYS LEU LYS LYS ALA LEU LYS ILE ALA ASN SEQRES 19 C 306 GLN CYS MET ASP PRO SER LEU GLN VAL GLN LEU PHE ILE SEQRES 20 C 306 GLU ILE LEU ASN ARG TYR ILE TYR PHE TYR GLU LYS GLU SEQRES 21 C 306 ASN ASP ALA VAL THR ILE GLN VAL LEU ASN GLN LEU ILE SEQRES 22 C 306 GLN LYS ILE ARG GLU ASP LEU PRO ASN LEU GLU SER SER SEQRES 23 C 306 GLU GLU THR GLU GLN ILE ASN LYS HIS PHE HIS ASN THR SEQRES 24 C 306 LEU GLU HIS LEU ARG LEU ARG SEQRES 1 D 306 MET VAL GLU ASP PRO ASP PRO GLU ASP PHE ALA ASP GLU SEQRES 2 D 306 GLN SER LEU VAL GLY ARG PHE ILE HIS LEU LEU ARG SER SEQRES 3 D 306 GLU ASP PRO ASP GLN GLN TYR LEU ILE LEU ASN THR ALA SEQRES 4 D 306 ARG LYS HIS PHE GLY ALA GLY GLY ASN GLN ARG ILE ARG SEQRES 5 D 306 PHE THR LEU PRO PRO LEU VAL PHE ALA ALA TYR GLN LEU SEQRES 6 D 306 ALA PHE ARG TYR LYS GLU ASN SER LYS VAL ASP ASP LYS SEQRES 7 D 306 TRP GLU LYS LYS CYS GLN LYS ILE PHE SER PHE ALA HIS SEQRES 8 D 306 GLN THR ILE SER ALA LEU ILE LYS ALA GLU LEU ALA GLU SEQRES 9 D 306 LEU PRO LEU ARG LEU PHE LEU GLN GLY ALA LEU ALA ALA SEQRES 10 D 306 GLY GLU ILE GLY PHE GLU ASN HIS GLU THR VAL ALA TYR SEQRES 11 D 306 GLU PHE MET SER GLN ALA PHE SER LEU TYR GLU ASP GLU SEQRES 12 D 306 ILE SER ASP SER LYS ALA GLN LEU ALA ALA ILE THR LEU SEQRES 13 D 306 ILE ILE GLY THR PHE GLU ARG MET LYS CYS PHE SER GLU SEQRES 14 D 306 GLU ASN HIS GLU PRO LEU ARG THR GLN CYS ALA LEU ALA SEQRES 15 D 306 ALA SER LYS LEU LEU LYS LYS PRO ASP GLN GLY ARG ALA SEQRES 16 D 306 VAL SER THR CYS ALA HIS LEU PHE TRP SER GLY ARG ASN SEQRES 17 D 306 THR ASP LYS ASN GLY GLU GLU LEU HIS GLY GLY LYS ARG SEQRES 18 D 306 VAL MET GLU CYS LEU LYS LYS ALA LEU LYS ILE ALA ASN SEQRES 19 D 306 GLN CYS MET ASP PRO SER LEU GLN VAL GLN LEU PHE ILE SEQRES 20 D 306 GLU ILE LEU ASN ARG TYR ILE TYR PHE TYR GLU LYS GLU SEQRES 21 D 306 ASN ASP ALA VAL THR ILE GLN VAL LEU ASN GLN LEU ILE SEQRES 22 D 306 GLN LYS ILE ARG GLU ASP LEU PRO ASN LEU GLU SER SER SEQRES 23 D 306 GLU GLU THR GLU GLN ILE ASN LYS HIS PHE HIS ASN THR SEQRES 24 D 306 LEU GLU HIS LEU ARG LEU ARG HET XFZ D 801 18 HETNAM XFZ BIS-1,3-PHENYL GUANYLHYDRAZON HETSYN XFZ 2-[(E)-[3-[(E)-[BIS(AZANYL) HETSYN 2 XFZ METHYLIDENEHYDRAZINYLIDENE]METHYL]PHENYL]METHYLIDENEAM HETSYN 3 XFZ INO]GUANIDINE FORMUL 5 XFZ C10 H14 N8 FORMUL 6 HOH *64(H2 O) HELIX 1 AA1 PRO A 19 LEU A 26 1 8 HELIX 2 AA2 THR A 42 ALA A 53 1 12 HELIX 3 AA3 ASP A 95 ASP A 107 1 13 HELIX 4 AA4 PRO B 19 LEU B 26 1 8 HELIX 5 AA5 THR B 42 ALA B 53 1 12 HELIX 6 AA6 ASP B 95 ASP B 107 1 13 HELIX 7 AA7 ASP C 480 ASP C 483 5 4 HELIX 8 AA8 PHE C 484 ARG C 499 1 16 HELIX 9 AA9 ASP C 502 ALA C 519 1 18 HELIX 10 AB1 GLY C 521 LEU C 529 1 9 HELIX 11 AB2 LEU C 529 ASN C 546 1 18 HELIX 12 AB3 LYS C 552 ALA C 574 1 23 HELIX 13 AB4 ALA C 577 GLY C 595 1 19 HELIX 14 AB5 ASN C 598 ILE C 618 1 21 HELIX 15 AB6 ASP C 620 ARG C 637 1 18 HELIX 16 AB7 SER C 642 LYS C 659 1 18 HELIX 17 AB8 LYS C 662 SER C 679 1 18 HELIX 18 AB9 GLY C 692 GLN C 709 1 18 HELIX 19 AC1 ASP C 712 LYS C 733 1 22 HELIX 20 AC2 THR C 739 LEU C 754 1 16 HELIX 21 AC3 PRO C 755 LEU C 757 5 3 HELIX 22 AC4 SER C 760 LEU C 779 1 20 HELIX 23 AC5 LEU D 490 LEU D 498 5 9 HELIX 24 AC6 ASP D 502 ALA D 519 1 18 HELIX 25 AC7 GLY D 521 LEU D 529 1 9 HELIX 26 AC8 LEU D 529 ASN D 546 1 18 HELIX 27 AC9 SER D 547 VAL D 549 5 3 HELIX 28 AD1 LYS D 552 ALA D 574 1 23 HELIX 29 AD2 ALA D 577 GLY D 595 1 19 HELIX 30 AD3 ASN D 598 ILE D 618 1 21 HELIX 31 AD4 ASP D 620 ARG D 637 1 18 HELIX 32 AD5 SER D 642 LYS D 659 1 18 HELIX 33 AD6 LYS D 662 SER D 679 1 18 HELIX 34 AD7 GLY D 692 GLN D 709 1 18 HELIX 35 AD8 ASP D 712 LYS D 733 1 22 HELIX 36 AD9 THR D 739 LEU D 754 1 16 HELIX 37 AE1 PRO D 755 LEU D 757 5 3 HELIX 38 AE2 SER D 760 ARG D 778 1 19 SHEET 1 AA1 6 VAL A 56 ILE A 58 0 SHEET 2 AA1 6 HIS A 33 CYS A 36 1 N CYS A 36 O HIS A 57 SHEET 3 AA1 6 LEU A 2 LEU A 6 1 N LEU A 4 O LEU A 35 SHEET 4 AA1 6 SER A 149 ASP A 154 -1 O VAL A 151 N VAL A 5 SHEET 5 AA1 6 THR A 159 ILE A 168 -1 O TYR A 163 N LEU A 152 SHEET 6 AA1 6 ASP A 171 LYS A 180 -1 O TYR A 179 N VAL A 160 SHEET 1 AA2 5 GLN A 72 VAL A 77 0 SHEET 2 AA2 5 PHE A 80 ILE A 85 -1 O ILE A 82 N VAL A 75 SHEET 3 AA2 5 ILE A 110 ILE A 112 1 O ILE A 112 N GLY A 83 SHEET 4 AA2 5 LYS A 127 ASN A 131 1 O PHE A 128 N LEU A 111 SHEET 5 AA2 5 GLU A 120 HIS A 124 -1 N GLU A 120 O ASN A 131 SHEET 1 AA3 6 VAL B 56 ILE B 58 0 SHEET 2 AA3 6 HIS B 33 CYS B 36 1 N CYS B 36 O HIS B 57 SHEET 3 AA3 6 LEU B 2 LEU B 6 1 N LEU B 4 O LEU B 35 SHEET 4 AA3 6 SER B 149 ILE B 155 -1 O MET B 153 N VAL B 3 SHEET 5 AA3 6 THR B 159 ILE B 168 -1 O TYR B 163 N LEU B 152 SHEET 6 AA3 6 ASP B 171 LYS B 180 -1 O ILE B 177 N THR B 162 SHEET 1 AA4 5 GLN B 72 VAL B 77 0 SHEET 2 AA4 5 PHE B 80 ILE B 85 -1 O ILE B 82 N VAL B 75 SHEET 3 AA4 5 ILE B 110 ILE B 112 1 O ILE B 112 N GLY B 83 SHEET 4 AA4 5 LYS B 127 ASN B 131 1 O PHE B 128 N LEU B 111 SHEET 5 AA4 5 GLU B 120 HIS B 124 -1 N GLU B 120 O ASN B 131 CISPEP 1 ILE A 11 PRO A 12 0 4.33 CISPEP 2 ILE A 91 PRO A 92 0 -5.84 CISPEP 3 ILE B 11 PRO B 12 0 5.02 CISPEP 4 ILE B 91 PRO B 92 0 -8.68 CRYST1 57.500 140.830 141.340 90.00 90.00 90.00 P 21 21 21 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 0.017391 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007075 0.00000