HEADER PROTEIN TRANSPORT 05-JAN-21 7L9X TITLE STRUCTURE OF VPS4B IN COMPLEX WITH AN ALLELE-SPECIFIC COVALENT TITLE 2 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CELL MIGRATION-INDUCING GENE 1 PROTEIN,SUPPRESSOR OF K(+) COMPND 5 TRANSPORT GROWTH DEFECT 1,PROTEIN SKD1; COMPND 6 EC: 3.6.4.6; COMPND 7 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: VPS4B, SKD1, VPS42, MIG1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHEMICAL INHIBITOR, HYDROLASE, ATPASE, AAA SUPERFAMILY, PROTEIN KEYWDS 2 TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.GRASSO,T.CUPIDO,T.M.KAPOOR REVDAT 3 18-OCT-23 7L9X 1 REMARK REVDAT 2 28-APR-21 7L9X 1 JRNL REVDAT 1 14-APR-21 7L9X 0 JRNL AUTH T.CUPIDO,N.H.JONES,M.J.GRASSO,R.PISA,T.M.KAPOOR JRNL TITL A CHEMICAL GENETICS APPROACH TO EXAMINE THE FUNCTIONS OF AAA JRNL TITL 2 PROTEINS. JRNL REF NAT.STRUCT.MOL.BIOL. V. 28 388 2021 JRNL REFN ESSN 1545-9985 JRNL PMID 33782614 JRNL DOI 10.1038/S41594-021-00575-9 REMARK 2 REMARK 2 RESOLUTION. 2.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 10979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1106 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 29.2400 - 5.6100 1.00 1261 143 0.1719 0.2220 REMARK 3 2 5.6100 - 4.4600 1.00 1257 140 0.1931 0.2337 REMARK 3 3 4.4600 - 3.9000 1.00 1246 134 0.1949 0.2541 REMARK 3 4 3.9000 - 3.5400 1.00 1245 142 0.2271 0.3254 REMARK 3 5 3.5400 - 3.2900 1.00 1255 141 0.2635 0.3265 REMARK 3 6 3.2900 - 3.1000 1.00 1230 137 0.2775 0.3402 REMARK 3 7 3.1000 - 2.9400 1.00 1267 142 0.3041 0.3634 REMARK 3 8 2.9400 - 2.8100 0.91 1112 127 0.4118 0.4670 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.479 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.859 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 94.94 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 94.66 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 2342 REMARK 3 ANGLE : 0.717 3183 REMARK 3 CHIRALITY : 0.043 364 REMARK 3 PLANARITY : 0.005 410 REMARK 3 DIHEDRAL : 8.851 1932 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 7L9X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253797. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11046 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.810 REMARK 200 RESOLUTION RANGE LOW (A) : 29.240 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.02234 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.6200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.87 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.35460 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: PHENIX REMARK 200 STARTING MODEL: 1XWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NH4SO4, 100 MM HEPES PH 7.5, REMARK 280 10% PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 88.55067 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 44.27533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 66.41300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.13767 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 110.68833 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 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 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 SER A 5 REMARK 465 PRO A 6 REMARK 465 ASN A 7 REMARK 465 LEU A 8 REMARK 465 GLN A 9 REMARK 465 LYS A 10 REMARK 465 ALA A 11 REMARK 465 ILE A 12 REMARK 465 ASP A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 LYS A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 GLN A 20 REMARK 465 GLU A 21 REMARK 465 ASP A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 GLY A 25 REMARK 465 ASN A 26 REMARK 465 TYR A 27 REMARK 465 GLU A 28 REMARK 465 GLU A 29 REMARK 465 ALA A 30 REMARK 465 LEU A 31 REMARK 465 GLN A 32 REMARK 465 LEU A 33 REMARK 465 TYR A 34 REMARK 465 GLN A 35 REMARK 465 HIS A 36 REMARK 465 ALA A 37 REMARK 465 VAL A 38 REMARK 465 GLN A 39 REMARK 465 TYR A 40 REMARK 465 PHE A 41 REMARK 465 LEU A 42 REMARK 465 HIS A 43 REMARK 465 VAL A 44 REMARK 465 VAL A 45 REMARK 465 LYS A 46 REMARK 465 TYR A 47 REMARK 465 GLU A 48 REMARK 465 ALA A 49 REMARK 465 GLN A 50 REMARK 465 GLY A 51 REMARK 465 ASP A 52 REMARK 465 LYS A 53 REMARK 465 ALA A 54 REMARK 465 LYS A 55 REMARK 465 GLN A 56 REMARK 465 SER A 57 REMARK 465 ILE A 58 REMARK 465 ARG A 59 REMARK 465 ALA A 60 REMARK 465 LYS A 61 REMARK 465 CYS A 62 REMARK 465 THR A 63 REMARK 465 GLU A 64 REMARK 465 TYR A 65 REMARK 465 LEU A 66 REMARK 465 ASP A 67 REMARK 465 ARG A 68 REMARK 465 ALA A 69 REMARK 465 GLU A 70 REMARK 465 LYS A 71 REMARK 465 LEU A 72 REMARK 465 LYS A 73 REMARK 465 GLU A 74 REMARK 465 TYR A 75 REMARK 465 LEU A 76 REMARK 465 LYS A 77 REMARK 465 ASN A 78 REMARK 465 LYS A 79 REMARK 465 GLU A 80 REMARK 465 LYS A 81 REMARK 465 LYS A 82 REMARK 465 ALA A 83 REMARK 465 GLN A 84 REMARK 465 LYS A 85 REMARK 465 PRO A 86 REMARK 465 VAL A 87 REMARK 465 LYS A 88 REMARK 465 GLU A 89 REMARK 465 GLY A 90 REMARK 465 GLN A 91 REMARK 465 PRO A 92 REMARK 465 SER A 93 REMARK 465 PRO A 94 REMARK 465 ALA A 95 REMARK 465 ASP A 96 REMARK 465 GLU A 97 REMARK 465 LYS A 98 REMARK 465 GLY A 99 REMARK 465 ASN A 100 REMARK 465 ASP A 101 REMARK 465 SER A 102 REMARK 465 ASP A 103 REMARK 465 GLY A 104 REMARK 465 GLU A 105 REMARK 465 GLY A 106 REMARK 465 GLU A 107 REMARK 465 SER A 108 REMARK 465 ASP A 109 REMARK 465 ASP A 110 REMARK 465 PRO A 111 REMARK 465 GLU A 112 REMARK 465 LYS A 113 REMARK 465 LYS A 114 REMARK 465 LYS A 115 REMARK 465 LEU A 116 REMARK 465 GLN A 117 REMARK 465 ASN A 118 REMARK 465 GLN A 119 REMARK 465 LEU A 120 REMARK 465 GLN A 121 REMARK 465 GLY A 122 REMARK 465 ALA A 123 REMARK 465 ILE A 124 REMARK 465 VAL A 125 REMARK 465 ASP A 203 REMARK 465 LEU A 204 REMARK 465 VAL A 205 REMARK 465 SER A 206 REMARK 465 LYS A 207 REMARK 465 TRP A 208 REMARK 465 LEU A 209 REMARK 465 GLY A 210 REMARK 465 GLU A 211 REMARK 465 GLY A 241 REMARK 465 SER A 242 REMARK 465 ARG A 243 REMARK 465 SER A 244 REMARK 465 GLU A 245 REMARK 465 ASN A 246 REMARK 465 GLU A 247 REMARK 465 GLY A 264 REMARK 465 VAL A 265 REMARK 465 GLY A 266 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 LYS A 132 CG CD CE NZ REMARK 470 LYS A 163 CG CD CE NZ REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 SER A 201 OG REMARK 470 GLU A 213 CG CD OE1 OE2 REMARK 470 LYS A 214 CG CD CE NZ REMARK 470 LEU A 215 CG CD1 CD2 REMARK 470 LYS A 217 CG CD CE NZ REMARK 470 ASN A 218 CG OD1 ND2 REMARK 470 PHE A 220 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 227 CE NZ REMARK 470 GLU A 249 CG CD OE1 OE2 REMARK 470 ARG A 253 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 254 CG1 CG2 CD1 REMARK 470 LYS A 255 CG CD CE NZ REMARK 470 GLU A 257 CG CD OE1 OE2 REMARK 470 PHE A 258 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 284 CG CD1 CD2 REMARK 470 GLU A 293 CG CD OE1 OE2 REMARK 470 LYS A 355 CG CD CE NZ REMARK 470 ASP A 388 CG OD1 OD2 REMARK 470 ARG A 416 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 429 CG OD1 OD2 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 NH2 ARG A 164 O LEU A 349 6554 2.06 REMARK 500 NZ LYS A 155 O VAL A 399 6554 2.19 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 VAL A 150 -50.29 -125.75 REMARK 500 ASN A 192 -47.42 58.12 REMARK 500 ASP A 237 -8.65 -59.54 REMARK 500 ASP A 270 -51.61 -123.81 REMARK 500 ILE A 280 77.79 -119.94 REMARK 500 THR A 333 76.80 -113.35 REMARK 500 PRO A 386 -3.27 -56.51 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 A 633 DISTANCE = 6.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XQV A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 DBREF 7L9X A 1 444 UNP O75351 VPS4B_HUMAN 1 444 SEQADV 7L9X SER A -1 UNP O75351 EXPRESSION TAG SEQADV 7L9X HIS A 0 UNP O75351 EXPRESSION TAG SEQADV 7L9X CYS A 135 UNP O75351 ASP 135 ENGINEERED MUTATION SEQRES 1 A 446 SER HIS MET SER SER THR SER PRO ASN LEU GLN LYS ALA SEQRES 2 A 446 ILE ASP LEU ALA SER LYS ALA ALA GLN GLU ASP LYS ALA SEQRES 3 A 446 GLY ASN TYR GLU GLU ALA LEU GLN LEU TYR GLN HIS ALA SEQRES 4 A 446 VAL GLN TYR PHE LEU HIS VAL VAL LYS TYR GLU ALA GLN SEQRES 5 A 446 GLY ASP LYS ALA LYS GLN SER ILE ARG ALA LYS CYS THR SEQRES 6 A 446 GLU TYR LEU ASP ARG ALA GLU LYS LEU LYS GLU TYR LEU SEQRES 7 A 446 LYS ASN LYS GLU LYS LYS ALA GLN LYS PRO VAL LYS GLU SEQRES 8 A 446 GLY GLN PRO SER PRO ALA ASP GLU LYS GLY ASN ASP SER SEQRES 9 A 446 ASP GLY GLU GLY GLU SER ASP ASP PRO GLU LYS LYS LYS SEQRES 10 A 446 LEU GLN ASN GLN LEU GLN GLY ALA ILE VAL ILE GLU ARG SEQRES 11 A 446 PRO ASN VAL LYS TRP SER CYS VAL ALA GLY LEU GLU GLY SEQRES 12 A 446 ALA LYS GLU ALA LEU LYS GLU ALA VAL ILE LEU PRO ILE SEQRES 13 A 446 LYS PHE PRO HIS LEU PHE THR GLY LYS ARG THR PRO TRP SEQRES 14 A 446 ARG GLY ILE LEU LEU PHE GLY PRO PRO GLY THR GLY LYS SEQRES 15 A 446 SER TYR LEU ALA LYS ALA VAL ALA THR GLU ALA ASN ASN SEQRES 16 A 446 SER THR PHE PHE SER ILE SER SER SER ASP LEU VAL SER SEQRES 17 A 446 LYS TRP LEU GLY GLU SER GLU LYS LEU VAL LYS ASN LEU SEQRES 18 A 446 PHE GLN LEU ALA ARG GLU ASN LYS PRO SER ILE ILE PHE SEQRES 19 A 446 ILE ASP GLU ILE ASP SER LEU CYS GLY SER ARG SER GLU SEQRES 20 A 446 ASN GLU SER GLU ALA ALA ARG ARG ILE LYS THR GLU PHE SEQRES 21 A 446 LEU VAL GLN MET GLN GLY VAL GLY VAL ASP ASN ASP GLY SEQRES 22 A 446 ILE LEU VAL LEU GLY ALA THR ASN ILE PRO TRP VAL LEU SEQRES 23 A 446 ASP SER ALA ILE ARG ARG ARG PHE GLU LYS ARG ILE TYR SEQRES 24 A 446 ILE PRO LEU PRO GLU PRO HIS ALA ARG ALA ALA MET PHE SEQRES 25 A 446 LYS LEU HIS LEU GLY THR THR GLN ASN SER LEU THR GLU SEQRES 26 A 446 ALA ASP PHE ARG GLU LEU GLY ARG LYS THR ASP GLY TYR SEQRES 27 A 446 SER GLY ALA ASP ILE SER ILE ILE VAL ARG ASP ALA LEU SEQRES 28 A 446 MET GLN PRO VAL ARG LYS VAL GLN SER ALA THR HIS PHE SEQRES 29 A 446 LYS LYS VAL ARG GLY PRO SER ARG ALA ASP PRO ASN HIS SEQRES 30 A 446 LEU VAL ASP ASP LEU LEU THR PRO CYS SER PRO GLY ASP SEQRES 31 A 446 PRO GLY ALA ILE GLU MET THR TRP MET ASP VAL PRO GLY SEQRES 32 A 446 ASP LYS LEU LEU GLU PRO VAL VAL SER MET SER ASP MET SEQRES 33 A 446 LEU ARG SER LEU SER ASN THR LYS PRO THR VAL ASN GLU SEQRES 34 A 446 HIS ASP LEU LEU LYS LEU LYS LYS PHE THR GLU ASP PHE SEQRES 35 A 446 GLY GLN GLU GLY HET XQV A 501 27 HET SO4 A 502 5 HETNAM XQV N-{3-[(8-PHENYL[1,2,4]TRIAZOLO[1,5-A]PYRIDIN-2-YL) HETNAM 2 XQV AMINO]PHENYL}PROPANAMIDE HETNAM SO4 SULFATE ION FORMUL 2 XQV C21 H19 N5 O FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *33(H2 O) HELIX 1 AA1 LYS A 132 VAL A 136 5 5 HELIX 2 AA2 LEU A 139 VAL A 150 1 12 HELIX 3 AA3 VAL A 150 PHE A 156 1 7 HELIX 4 AA4 GLY A 179 ASN A 192 1 14 HELIX 5 AA5 GLU A 213 ASN A 226 1 14 HELIX 6 AA6 GLU A 235 LEU A 239 5 5 HELIX 7 AA7 ALA A 250 LYS A 255 1 6 HELIX 8 AA8 THR A 256 GLN A 263 1 8 HELIX 9 AA9 ASP A 285 ARG A 290 1 6 HELIX 10 AB1 GLU A 302 HIS A 313 1 12 HELIX 11 AB2 THR A 322 THR A 333 1 12 HELIX 12 AB3 SER A 337 MET A 350 1 14 HELIX 13 AB4 MET A 350 ALA A 359 1 10 HELIX 14 AB5 THR A 395 VAL A 399 5 5 HELIX 15 AB6 PRO A 400 LEU A 404 5 5 HELIX 16 AB7 SER A 410 SER A 419 1 10 HELIX 17 AB8 ASN A 426 PHE A 440 1 15 SHEET 1 AA1 5 PHE A 196 ILE A 199 0 SHEET 2 AA1 5 SER A 229 ILE A 233 1 O PHE A 232 N ILE A 199 SHEET 3 AA1 5 ILE A 272 THR A 278 1 O LEU A 275 N ILE A 233 SHEET 4 AA1 5 GLY A 169 PHE A 173 1 N LEU A 172 O GLY A 276 SHEET 5 AA1 5 LYS A 294 TYR A 297 1 O ILE A 296 N LEU A 171 SHEET 1 AA2 3 LEU A 376 PRO A 383 0 SHEET 2 AA2 3 HIS A 361 PRO A 368 -1 N GLY A 367 O VAL A 377 SHEET 3 AA2 3 ILE A 392 GLU A 393 -1 O ILE A 392 N PHE A 362 LINK SG CYS A 135 C01 XQV A 501 1555 1555 1.30 CISPEP 1 LYS A 227 PRO A 228 0 -1.77 SITE 1 AC1 12 CYS A 135 ALA A 137 GLY A 177 THR A 178 SITE 2 AC1 12 GLY A 179 TYR A 182 MET A 309 LEU A 312 SITE 3 AC1 12 HIS A 313 GLY A 338 ALA A 339 SO4 A 502 SITE 1 AC2 7 GLY A 177 THR A 178 GLY A 179 LYS A 180 SITE 2 AC2 7 SER A 181 XQV A 501 HOH A 605 CRYST1 77.876 77.876 132.826 90.00 90.00 120.00 P 65 6 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 0.012841 0.007414 0.000000 0.00000 SCALE2 0.000000 0.014827 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007529 0.00000