HEADER HYDROLASE 08-NOV-22 8HET TITLE CRYSTAL STRUCTURE OF CTSL IN COMPLEX WITH E64D COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROCATHEPSIN L; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CATHEPESIN L; COMPND 5 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: CTSL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR, ANTIVIRAL, PROTEASE, ANTIVIRAL PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,M.SHAO,L.SUN,H.YANG REVDAT 1 13-DEC-23 8HET 0 JRNL AUTH H.WANG,M.SHAO,L.SUN,H.YANG JRNL TITL CRYSTAL STRUCTURE OF CTSB IN COMPLEX WITH K777 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 15707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1571 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 42.2200 - 4.4500 1.00 1385 158 0.1786 0.1820 REMARK 3 2 4.4400 - 3.5300 1.00 1323 144 0.1477 0.1652 REMARK 3 3 3.5300 - 3.0800 1.00 1277 145 0.1733 0.2144 REMARK 3 4 3.0800 - 2.8000 1.00 1287 141 0.1935 0.2373 REMARK 3 5 2.8000 - 2.6000 1.00 1285 142 0.2124 0.2502 REMARK 3 6 2.6000 - 2.4500 1.00 1274 139 0.2014 0.2538 REMARK 3 7 2.4500 - 2.3300 1.00 1253 146 0.1956 0.2547 REMARK 3 8 2.3200 - 2.2200 1.00 1252 141 0.1976 0.2685 REMARK 3 9 2.2200 - 2.1400 1.00 1277 138 0.2040 0.2415 REMARK 3 10 2.1400 - 2.0600 1.00 1268 137 0.2153 0.2723 REMARK 3 11 2.0600 - 2.0000 1.00 1255 140 0.2326 0.2451 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.230 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 : 0.006 1735 REMARK 3 ANGLE : 0.898 2351 REMARK 3 CHIRALITY : 0.060 237 REMARK 3 PLANARITY : 0.008 313 REMARK 3 DIHEDRAL : 17.046 616 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 8HET COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1300033488. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-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 : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9784 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M 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 : 15716 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 42.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.81 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.94400 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: 5MAJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM CITRIC ACID, 3M SODIUM CHLORIDE, REMARK 280 PH 3.5, VAPOR DIFFUSION, HANGING 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 23.27100 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.18100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.85250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.18100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.27100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.85250 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 GLU A 176 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 10 CE NZ REMARK 470 LYS A 120 CD CE NZ REMARK 470 LYS A 124 CD CE NZ REMARK 470 ASP A 160 CG OD1 OD2 REMARK 470 GLU A 173 CG CD OE1 OE2 REMARK 470 SER A 174 OG REMARK 470 SER A 177 OG REMARK 470 ARG A 206 CG CD NE CZ NH1 NH2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 3 CZ REMARK 480 GLU A 191 CD 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 209 18.33 56.51 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HET A 1 220 UNP P07711 CATL1_HUMAN 114 333 SEQRES 1 A 220 ALA PRO ARG SER VAL ASP TRP ARG GLU LYS GLY TYR VAL SEQRES 2 A 220 THR PRO VAL LYS ASN GLN GLY GLN CYS GLY SER CYS TRP SEQRES 3 A 220 ALA PHE SER ALA THR GLY ALA LEU GLU GLY GLN MET PHE SEQRES 4 A 220 ARG LYS THR GLY ARG LEU ILE SER LEU SER GLU GLN ASN SEQRES 5 A 220 LEU VAL ASP CYS SER GLY PRO GLN GLY ASN GLU GLY CYS SEQRES 6 A 220 ASN GLY GLY LEU MET ASP TYR ALA PHE GLN TYR VAL GLN SEQRES 7 A 220 ASP ASN GLY GLY LEU ASP SER GLU GLU SER TYR PRO TYR SEQRES 8 A 220 GLU ALA THR GLU GLU SER CYS LYS TYR ASN PRO LYS TYR SEQRES 9 A 220 SER VAL ALA ASN ASP THR GLY PHE VAL ASP ILE PRO LYS SEQRES 10 A 220 GLN GLU LYS ALA LEU MET LYS ALA VAL ALA THR VAL GLY SEQRES 11 A 220 PRO ILE SER VAL ALA ILE ASP ALA GLY HIS GLU SER PHE SEQRES 12 A 220 LEU PHE TYR LYS GLU GLY ILE TYR PHE GLU PRO ASP CYS SEQRES 13 A 220 SER SER GLU ASP MET ASP HIS GLY VAL LEU VAL VAL GLY SEQRES 14 A 220 TYR GLY PHE GLU SER THR GLU SER ASP ASN ASN LYS TYR SEQRES 15 A 220 TRP LEU VAL LYS ASN SER TRP GLY GLU GLU TRP GLY MET SEQRES 16 A 220 GLY GLY TYR VAL LYS MET ALA LYS ASP ARG ARG ASN HIS SEQRES 17 A 220 CYS GLY ILE ALA SER ALA ALA SER TYR PRO THR VAL HET E6D A 301 24 HETNAM E6D ETHYL (3S)-3-HYDROXY-4-({(2S)-4-METHYL-1-[(3- HETNAM 2 E6D METHYLBUTYL)AMINO]-1-OXOPENTAN-2-YL}AMINO)-4- HETNAM 3 E6D OXOBUTANOATE FORMUL 2 E6D C17 H32 N2 O5 FORMUL 3 HOH *170(H2 O) HELIX 1 AA1 ARG A 8 GLY A 11 5 4 HELIX 2 AA2 SER A 24 GLY A 43 1 20 HELIX 3 AA3 SER A 49 SER A 57 1 9 HELIX 4 AA4 GLY A 58 GLY A 61 5 4 HELIX 5 AA5 GLU A 63 GLY A 67 5 5 HELIX 6 AA6 LEU A 69 GLY A 81 1 13 HELIX 7 AA7 ASN A 101 LYS A 103 5 3 HELIX 8 AA8 GLN A 118 VAL A 129 1 12 HELIX 9 AA9 HIS A 140 PHE A 145 1 6 HELIX 10 AB1 ASN A 207 ILE A 211 5 5 SHEET 1 AA1 3 VAL A 5 ASP A 6 0 SHEET 2 AA1 3 HIS A 163 PHE A 172 -1 O TYR A 170 N VAL A 5 SHEET 3 AA1 3 ILE A 132 ILE A 136 -1 N ILE A 132 O VAL A 167 SHEET 1 AA2 5 VAL A 5 ASP A 6 0 SHEET 2 AA2 5 HIS A 163 PHE A 172 -1 O TYR A 170 N VAL A 5 SHEET 3 AA2 5 LYS A 181 LYS A 186 -1 O LYS A 186 N LEU A 166 SHEET 4 AA2 5 TYR A 198 ALA A 202 -1 O MET A 201 N TRP A 183 SHEET 5 AA2 5 ILE A 150 TYR A 151 1 N TYR A 151 O LYS A 200 SHEET 1 AA3 2 LEU A 83 ASP A 84 0 SHEET 2 AA3 2 SER A 105 ALA A 107 -1 O VAL A 106 N LEU A 83 SHEET 1 AA4 2 GLY A 111 ASP A 114 0 SHEET 2 AA4 2 SER A 216 THR A 219 -1 O TYR A 217 N VAL A 113 SSBOND 1 CYS A 22 CYS A 65 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 98 1555 1555 2.05 SSBOND 3 CYS A 156 CYS A 209 1555 1555 2.08 LINK SG CYS A 25 C2 E6D A 301 1555 1555 1.82 CRYST1 46.542 47.705 100.362 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 0.021486 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020962 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009964 0.00000