HEADER HYDROLASE 11-FEB-25 9NAE TITLE MICROED STRUCTURE OF PAPAIN CO-CRYSTALLIZED WITH E-64 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PAPAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PAPAYA PROTEINASE I,PPI; COMPND 5 EC: 3.4.22.2 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CARICA PAPAYA; SOURCE 3 ORGANISM_COMMON: PAPAYA; SOURCE 4 ORGANISM_TAXID: 3649 KEYWDS INHIBITOR, COMPLEX, MICROED, PROTEASE, HYDROLASE EXPDTA ELECTRON CRYSTALLOGRAPHY AUTHOR N.VLAHAKIS,J.A.RODRIGUEZ REVDAT 1 26-MAR-25 9NAE 0 JRNL AUTH N.W.VLAHAKIS,C.W.FLOWERS,M.LIU,M.AGDANOWSKI,S.JOHNSON, JRNL AUTH 2 J.A.SUMMERS,C.KEYSER,P.RUSSELL,S.ROSE,J.ORLANS,N.ADHAMI, JRNL AUTH 3 Y.CHEN,M.R.SAWAYA,S.BASU,D.DE SANCTIS,S.WAKATSUKI, JRNL AUTH 4 H.M.NELSON,J.A.LOO,Y.TANG,J.A.RODRIGUEZ JRNL TITL COMBINING MICROED AND NATIVE MASS SPECTROMETRY FOR JRNL TITL 2 STRUCTURAL DISCOVERY OF ENZYME-BIOSYNTHETIC INHIBITOR JRNL TITL 3 COMPLEXES. JRNL REF BIORXIV 2025 JRNL REFN ISSN 2692-8205 JRNL PMID 40060639 JRNL DOI 10.1101/2025.02.20.638743 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 8983 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.030 REMARK 3 FREE R VALUE TEST SET COUNT : 901 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 50.3400 - 4.1800 0.88 1382 155 0.1680 0.2017 REMARK 3 2 4.1800 - 3.3200 0.92 1358 151 0.1661 0.2192 REMARK 3 3 3.3200 - 2.9000 0.92 1337 149 0.2146 0.2842 REMARK 3 4 2.9000 - 2.6300 0.93 1349 151 0.2475 0.3194 REMARK 3 5 2.6300 - 2.4400 0.92 1330 148 0.2736 0.3128 REMARK 3 6 2.4400 - 2.3000 0.92 1326 147 0.2730 0.3495 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.250 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.26 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 : 0.007 1720 REMARK 3 ANGLE : 0.959 2335 REMARK 3 CHIRALITY : 0.065 235 REMARK 3 PLANARITY : 0.008 307 REMARK 3 DIHEDRAL : 7.152 250 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 9NAE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-FEB-25. REMARK 100 THE DEPOSITION ID IS D_1000292879. REMARK 240 REMARK 240 EXPERIMENTAL DETAILS REMARK 240 RECONSTRUCTION METHOD : CRYSTALLOGRAPHY REMARK 240 SAMPLE TYPE : 3D ARRAY REMARK 240 SPECIMEN TYPE : NULL REMARK 240 DATA ACQUISITION REMARK 240 DATE OF DATA COLLECTION : NULL REMARK 240 TEMPERATURE (KELVIN) : NULL REMARK 240 PH : NULL REMARK 240 NUMBER OF CRYSTALS USED : NULL REMARK 240 MICROSCOPE MODEL : TFS TALOS F200C REMARK 240 DETECTOR TYPE : DIRECT ELECTRON APOLLO (4K X REMARK 240 4K) REMARK 240 ACCELERATION VOLTAGE (KV) : 200 REMARK 240 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 240 RESOLUTION RANGE HIGH (A) : NULL REMARK 240 RESOLUTION RANGE LOW (A) : NULL REMARK 240 DATA SCALING SOFTWARE : XSCALE REMARK 240 COMPLETENESS FOR RANGE (%) : NULL REMARK 240 DATA REDUNDANCY : NULL REMARK 240 IN THE HIGHEST RESOLUTION SHELL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) :NULL REMARK 240 HIGHEST RESOLUTION SHELL, RANGE LOW (A) :NULL REMARK 240 COMPLETENESS FOR SHELL (%) : NULL REMARK 240 DATA REDUNDANCY IN SHELL : NULL REMARK 240 R MERGE FOR SHELL (I) : NULL REMARK 240 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 240 SOFTWARE USED : PHASER REMARK 240 STARTING MODEL : NULL 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 21.09000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.34500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.34500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.09000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.62500 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 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 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 139 CD CE NZ 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 TYR A 78 -69.87 -108.75 REMARK 500 ASP A 158 7.71 -152.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9N9D RELATED DB: PDB REMARK 900 SAME PROTEIN COMPLEXED WITH DIFFERENT LIGAND DBREF 9NAE A 1 212 UNP P00784 PAPA1_CARPA 134 345 SEQRES 1 A 212 ILE PRO GLU TYR VAL ASP TRP ARG GLN LYS GLY ALA VAL SEQRES 2 A 212 THR PRO VAL LYS ASN GLN GLY SER CYS GLY SER CYS TRP SEQRES 3 A 212 ALA PHE SER ALA VAL VAL THR ILE GLU GLY ILE ILE LYS SEQRES 4 A 212 ILE ARG THR GLY ASN LEU ASN GLU TYR SER GLU GLN GLU SEQRES 5 A 212 LEU LEU ASP CYS ASP ARG ARG SER TYR GLY CYS ASN GLY SEQRES 6 A 212 GLY TYR PRO TRP SER ALA LEU GLN LEU VAL ALA GLN TYR SEQRES 7 A 212 GLY ILE HIS TYR ARG ASN THR TYR PRO TYR GLU GLY VAL SEQRES 8 A 212 GLN ARG TYR CYS ARG SER ARG GLU LYS GLY PRO TYR ALA SEQRES 9 A 212 ALA LYS THR ASP GLY VAL ARG GLN VAL GLN PRO TYR ASN SEQRES 10 A 212 GLU GLY ALA LEU LEU TYR SER ILE ALA ASN GLN PRO VAL SEQRES 11 A 212 SER VAL VAL LEU GLU ALA ALA GLY LYS ASP PHE GLN LEU SEQRES 12 A 212 TYR ARG GLY GLY ILE PHE VAL GLY PRO CYS GLY ASN LYS SEQRES 13 A 212 VAL ASP HIS ALA VAL ALA ALA VAL GLY TYR GLY PRO ASN SEQRES 14 A 212 TYR ILE LEU ILE LYS ASN SER TRP GLY THR GLY TRP GLY SEQRES 15 A 212 GLU ASN GLY TYR ILE ARG ILE LYS ARG GLY THR GLY ASN SEQRES 16 A 212 SER TYR GLY VAL CYS GLY LEU TYR THR SER SER PHE TYR SEQRES 17 A 212 PRO VAL LYS ASN HET E64 A 301 25 HETNAM E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO- HETNAM 2 E64 BUTYL]-GUANIDINE FORMUL 2 E64 C15 H30 N5 O5 1+ FORMUL 3 HOH *22(H2 O) HELIX 1 AA1 SER A 24 GLY A 43 1 20 HELIX 2 AA2 SER A 49 ASP A 57 1 9 HELIX 3 AA3 TYR A 61 GLY A 65 5 5 HELIX 4 AA4 TYR A 67 TYR A 78 1 12 HELIX 5 AA5 SER A 97 GLY A 101 5 5 HELIX 6 AA6 ASN A 117 GLN A 128 1 12 HELIX 7 AA7 GLY A 138 LEU A 143 1 6 HELIX 8 AA8 GLY A 198 LEU A 202 5 5 SHEET 1 AA1 3 VAL A 5 ASP A 6 0 SHEET 2 AA1 3 HIS A 159 GLY A 167 -1 O TYR A 166 N VAL A 5 SHEET 3 AA1 3 VAL A 130 LEU A 134 -1 N VAL A 130 O ALA A 163 SHEET 1 AA2 5 VAL A 5 ASP A 6 0 SHEET 2 AA2 5 HIS A 159 GLY A 167 -1 O TYR A 166 N VAL A 5 SHEET 3 AA2 5 TYR A 170 LYS A 174 -1 O TYR A 170 N GLY A 167 SHEET 4 AA2 5 TYR A 186 LYS A 190 -1 O ILE A 187 N ILE A 173 SHEET 5 AA2 5 ILE A 148 PHE A 149 1 N PHE A 149 O ARG A 188 SHEET 1 AA3 2 GLY A 109 GLN A 112 0 SHEET 2 AA3 2 PHE A 207 VAL A 210 -1 O TYR A 208 N ARG A 111 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 95 1555 1555 2.05 SSBOND 3 CYS A 153 CYS A 200 1555 1555 2.06 LINK SG CYS A 25 C2 E64 A 301 1555 1555 1.80 CISPEP 1 GLY A 151 PRO A 152 0 3.37 CRYST1 42.180 49.250 100.690 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 0.023708 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020305 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009931 0.00000 TER 1653 ASN A 212 HETATM 1654 C1 E64 A 301 2.688 14.164 15.836 0.73 24.35 C HETATM 1655 O1 E64 A 301 3.663 14.892 16.059 0.73 24.27 O HETATM 1656 O2 E64 A 301 2.063 14.103 14.736 0.73 21.82 O HETATM 1657 C2 E64 A 301 2.175 13.248 16.953 0.73 27.81 C HETATM 1658 C3 E64 A 301 0.704 13.397 17.340 0.73 25.59 C HETATM 1659 O3 E64 A 301 0.465 14.667 17.898 0.73 29.90 O HETATM 1660 C4 E64 A 301 0.299 12.224 18.249 0.73 24.28 C HETATM 1661 O4 E64 A 301 -0.143 11.187 17.785 0.73 20.98 O HETATM 1662 N1 E64 A 301 0.469 12.363 19.567 0.73 29.24 N HETATM 1663 C6 E64 A 301 0.115 11.268 20.450 0.73 30.89 C HETATM 1664 C7 E64 A 301 1.177 11.074 21.511 0.73 36.08 C HETATM 1665 C8 E64 A 301 1.635 9.626 21.636 0.73 32.37 C HETATM 1666 C9 E64 A 301 1.695 8.997 20.246 0.73 29.36 C HETATM 1667 C10 E64 A 301 2.995 9.579 22.311 0.73 29.89 C HETATM 1668 C11 E64 A 301 -1.238 11.509 21.112 0.73 26.81 C HETATM 1669 O5 E64 A 301 -1.510 12.590 21.616 0.73 28.82 O HETATM 1670 N2 E64 A 301 -2.057 10.449 21.077 0.73 26.76 N HETATM 1671 C12 E64 A 301 -3.392 10.435 21.629 0.73 25.19 C HETATM 1672 C13 E64 A 301 -4.399 11.091 20.689 0.73 34.19 C HETATM 1673 C14 E64 A 301 -5.486 11.863 21.413 0.73 40.41 C HETATM 1674 C15 E64 A 301 -5.383 13.373 21.221 0.73 43.63 C HETATM 1675 N3 E64 A 301 -6.414 13.911 20.347 0.73 43.72 N HETATM 1676 C16 E64 A 301 -7.733 13.869 20.577 0.73 42.21 C HETATM 1677 N4 E64 A 301 -8.255 13.314 21.659 0.73 34.84 N HETATM 1678 N5 E64 A 301 -8.568 14.408 19.678 0.73 32.17 N HETATM 1679 O HOH A 401 8.933 4.629 23.668 1.00 16.58 O HETATM 1680 O HOH A 402 -11.924 9.066 8.465 1.00 21.15 O HETATM 1681 O HOH A 403 5.206 16.473 15.053 1.00 15.82 O HETATM 1682 O HOH A 404 16.124 -5.985 29.822 1.00 18.44 O HETATM 1683 O HOH A 405 2.762 -5.573 -0.174 1.00 17.38 O HETATM 1684 O HOH A 406 7.347 9.755 13.304 1.00 11.43 O HETATM 1685 O HOH A 407 17.634 6.697 26.203 1.00 12.31 O HETATM 1686 O HOH A 408 10.435 -8.274 21.069 1.00 18.61 O HETATM 1687 O HOH A 409 21.015 9.465 9.181 1.00 17.65 O HETATM 1688 O HOH A 410 7.569 -9.504 15.017 1.00 24.54 O HETATM 1689 O HOH A 411 -5.251 9.477 0.069 1.00 16.81 O HETATM 1690 O HOH A 412 17.505 0.861 3.129 1.00 22.44 O HETATM 1691 O HOH A 413 -11.453 11.844 13.522 1.00 19.91 O HETATM 1692 O HOH A 414 10.815 0.618 7.450 1.00 16.73 O HETATM 1693 O HOH A 415 17.764 21.785 7.402 1.00 25.49 O HETATM 1694 O HOH A 416 7.683 -11.032 12.804 1.00 20.39 O HETATM 1695 O HOH A 417 24.160 -5.024 8.302 1.00 35.70 O HETATM 1696 O HOH A 418 4.463 3.663 20.261 1.00 15.56 O HETATM 1697 O HOH A 419 -6.822 -2.197 3.708 1.00 17.40 O HETATM 1698 O HOH A 420 21.288 -4.367 10.904 1.00 16.44 O HETATM 1699 O HOH A 421 10.061 17.999 3.425 1.00 18.27 O HETATM 1700 O HOH A 422 -9.275 -2.403 4.622 1.00 22.79 O CONECT 173 493 CONECT 189 1657 CONECT 435 760 CONECT 493 173 CONECT 760 435 CONECT 1200 1554 CONECT 1554 1200 CONECT 1654 1655 1656 1657 CONECT 1655 1654 CONECT 1656 1654 CONECT 1657 189 1654 1658 CONECT 1658 1657 1659 1660 CONECT 1659 1658 CONECT 1660 1658 1661 1662 CONECT 1661 1660 CONECT 1662 1660 1663 CONECT 1663 1662 1664 1668 CONECT 1664 1663 1665 CONECT 1665 1664 1666 1667 CONECT 1666 1665 CONECT 1667 1665 CONECT 1668 1663 1669 1670 CONECT 1669 1668 CONECT 1670 1668 1671 CONECT 1671 1670 1672 CONECT 1672 1671 1673 CONECT 1673 1672 1674 CONECT 1674 1673 1675 CONECT 1675 1674 1676 CONECT 1676 1675 1677 1678 CONECT 1677 1676 CONECT 1678 1676 MASTER 197 0 1 8 10 0 0 6 1699 1 32 17 END