HEADER ANTIVIRAL PROTEIN/INHIBITOR 08-NOV-22 8HEN TITLE CRYSTAL STRUCTURE OF CTSB IN COMPLEX WITH 212-148 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: APP SECRETASE,APPS,CATHEPSIN B1; COMPND 5 EC: 3.4.22.1; COMPND 6 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: CTSB, CPSB; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, ANTIVIRAL, PROTEASE, ANTIVIRAL PROTEIN, ANTIVIRAL PROTEIN- KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,D.LI,L.SUN,H.YANG REVDAT 1 13-DEC-23 8HEN 0 JRNL AUTH H.WANG,D.LI,L.SUN,H.YANG JRNL TITL CRYSTAL STRUCTURE OF CTSB IN COMPLEX WITH 212-148 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1-4487-000 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.880 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 18380 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 1837 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 37.4700 - 4.5900 0.99 1388 153 0.1703 0.2082 REMARK 3 2 4.5800 - 3.6400 1.00 1322 147 0.1452 0.1709 REMARK 3 3 3.6400 - 3.1800 1.00 1290 143 0.1641 0.2179 REMARK 3 4 3.1800 - 2.8900 1.00 1291 144 0.1927 0.2380 REMARK 3 5 2.8900 - 2.6800 1.00 1271 142 0.1863 0.2387 REMARK 3 6 2.6800 - 2.5200 1.00 1271 141 0.1967 0.2437 REMARK 3 7 2.5200 - 2.4000 1.00 1251 138 0.2022 0.2498 REMARK 3 8 2.4000 - 2.2900 1.00 1276 140 0.1983 0.2809 REMARK 3 9 2.2900 - 2.2000 1.00 1256 140 0.2100 0.2434 REMARK 3 10 2.2000 - 2.1300 1.00 1252 139 0.2264 0.3020 REMARK 3 11 2.1300 - 2.0600 0.99 1244 139 0.2318 0.3026 REMARK 3 12 2.0600 - 2.0000 0.99 1245 138 0.2624 0.2628 REMARK 3 13 2.0000 - 1.9500 0.97 1186 133 0.2818 0.3868 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.970 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 : 0.008 2079 REMARK 3 ANGLE : 0.967 2826 REMARK 3 CHIRALITY : 0.065 278 REMARK 3 PLANARITY : 0.008 370 REMARK 3 DIHEDRAL : 16.302 725 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 8HEN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-AUG-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL10U2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS 2020-12-02 REMARK 200 DATA SCALING SOFTWARE : XDS 2020-12-02 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18398 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 37.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.090 REMARK 200 R MERGE (I) : 0.14800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.87100 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 1.20.1-4487-000 REMARK 200 STARTING MODEL: 6AY2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M NAAC PH 5.2, 28% W/V PEG 3350, VAPOR DIFFUSION, HANGING REMARK 280 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 15.73850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.34350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 40.79850 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.34350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.73850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 40.79850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 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 ASP A -2 REMARK 465 LEU A -1 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 GLU A 122 CG CD OE1 OE2 REMARK 470 LYS A 127 CG CD CE NZ REMARK 470 LYS A 158 CG CD CE NZ REMARK 470 GLU A 194 CG CD OE1 OE2 REMARK 470 ASP A 254 CG OD1 OD2 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 THR A 120 -169.71 -120.24 REMARK 500 ASN A 222 176.36 67.66 REMARK 500 CYS A 240 18.91 59.65 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HEN A -2 254 UNP P07858 CATB_HUMAN 77 333 SEQRES 1 A 257 ASP LEU LYS LEU PRO ALA SER PHE ASP ALA ARG GLU GLN SEQRES 2 A 257 TRP PRO GLN CYS PRO THR ILE LYS GLU ILE ARG ASP GLN SEQRES 3 A 257 GLY SER CYS GLY SER CYS TRP ALA PHE GLY ALA VAL GLU SEQRES 4 A 257 ALA ILE SER ASP ARG ILE CYS ILE HIS THR ASN ALA HIS SEQRES 5 A 257 VAL SER VAL GLU VAL SER ALA GLU ASP LEU LEU THR CYS SEQRES 6 A 257 CYS GLY SER MET CYS GLY ASP GLY CYS ASN GLY GLY TYR SEQRES 7 A 257 PRO ALA GLU ALA TRP ASN PHE TRP THR ARG LYS GLY LEU SEQRES 8 A 257 VAL SER GLY GLY LEU TYR GLU SER HIS VAL GLY CYS ARG SEQRES 9 A 257 PRO TYR SER ILE PRO PRO CYS GLU HIS HIS VAL ASN GLY SEQRES 10 A 257 SER ARG PRO PRO CYS THR GLY GLU GLY ASP THR PRO LYS SEQRES 11 A 257 CYS SER LYS ILE CYS GLU PRO GLY TYR SER PRO THR TYR SEQRES 12 A 257 LYS GLN ASP LYS HIS TYR GLY TYR ASN SER TYR SER VAL SEQRES 13 A 257 SER ASN SER GLU LYS ASP ILE MET ALA GLU ILE TYR LYS SEQRES 14 A 257 ASN GLY PRO VAL GLU GLY ALA PHE SER VAL TYR SER ASP SEQRES 15 A 257 PHE LEU LEU TYR LYS SER GLY VAL TYR GLN HIS VAL THR SEQRES 16 A 257 GLY GLU MET MET GLY GLY HIS ALA ILE ARG ILE LEU GLY SEQRES 17 A 257 TRP GLY VAL GLU ASN GLY THR PRO TYR TRP LEU VAL ALA SEQRES 18 A 257 ASN SER TRP ASN THR ASP TRP GLY ASP ASN GLY PHE PHE SEQRES 19 A 257 LYS ILE LEU ARG GLY GLN ASP HIS CYS GLY ILE GLU SER SEQRES 20 A 257 GLU VAL VAL ALA GLY ILE PRO ARG THR ASP HET GOL A 301 6 HET GOL A 302 6 HET DMS A 303 4 HET L4F A 304 55 HETNAM GOL GLYCEROL HETNAM DMS DIMETHYL SULFOXIDE HETNAM L4F 2-[4-[[(2~{S})-1-OXIDANYLIDENE-3-PHENYL-1-[[(3~{S})-1- HETNAM 2 L4F PHENYL-5-(PHENYLSULFONYL)PENTAN-3-YL]AMINO]PROPAN-2- HETNAM 3 L4F YL]CARBAMOYL]PIPERAZIN-1-YL]ETHYL 4- HETNAM 4 L4F CARBAMIMIDAMIDOBENZOATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 DMS C2 H6 O S FORMUL 5 L4F C41 H49 N7 O6 S FORMUL 6 HOH *139(H2 O) HELIX 1 AA1 ALA A 7 TRP A 11 1 5 HELIX 2 AA2 CYS A 14 GLU A 19 5 6 HELIX 3 AA3 SER A 28 THR A 46 1 19 HELIX 4 AA4 SER A 55 CYS A 63 1 9 HELIX 5 AA5 GLY A 64 CYS A 67 5 4 HELIX 6 AA6 ASP A 69 GLY A 73 5 5 HELIX 7 AA7 TYR A 75 LYS A 86 1 12 HELIX 8 AA8 SER A 156 GLY A 168 1 13 HELIX 9 AA9 ASP A 179 TYR A 183 5 5 HELIX 10 AB1 ASP A 238 ILE A 242 5 5 SHEET 1 AA1 3 PHE A 5 ASP A 6 0 SHEET 2 AA1 3 MET A 195 GLU A 209 -1 O TRP A 206 N PHE A 5 SHEET 3 AA1 3 VAL A 170 TYR A 177 -1 N VAL A 176 O MET A 196 SHEET 1 AA2 5 PHE A 5 ASP A 6 0 SHEET 2 AA2 5 MET A 195 GLU A 209 -1 O TRP A 206 N PHE A 5 SHEET 3 AA2 5 THR A 212 ALA A 218 -1 O ALA A 218 N ARG A 202 SHEET 4 AA2 5 PHE A 230 LEU A 234 -1 O ILE A 233 N TRP A 215 SHEET 5 AA2 5 VAL A 187 TYR A 188 1 N TYR A 188 O LYS A 232 SHEET 1 AA3 2 TYR A 151 SER A 152 0 SHEET 2 AA3 2 VAL A 247 ALA A 248 -1 O ALA A 248 N TYR A 151 SSBOND 1 CYS A 14 CYS A 43 1555 1555 2.07 SSBOND 2 CYS A 26 CYS A 71 1555 1555 2.05 SSBOND 3 CYS A 62 CYS A 128 1555 1555 2.05 SSBOND 4 CYS A 63 CYS A 67 1555 1555 2.02 SSBOND 5 CYS A 100 CYS A 132 1555 1555 2.04 SSBOND 6 CYS A 108 CYS A 119 1555 1555 2.03 LINK SG CYS A 29 C18 L4F A 304 1555 1555 1.82 CRYST1 31.477 81.597 94.687 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.031769 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012255 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010561 0.00000