HEADER STRUCTURAL PROTEIN/INHIBITOR 30-JUN-19 6KD5 TITLE CRYSTAL STRUCTURE OF THE EXTRACELLULAR DOMAIN OF MSPL/TMPRSS13 IN TITLE 2 COMPLEX WITH DEC-RVKR-CMK INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSMEMBRANE PROTEASE SERINE 13; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 192-325; COMPND 5 SYNONYM: MEMBRANE-TYPE MOSAIC SERINE PROTEASE,MOSAIC SERINE PROTEASE; COMPND 6 EC: 3.4.21.-; COMPND 7 ENGINEERED: YES; COMPND 8 OTHER_DETAILS: NON-CATALYTIC CHAIN; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: TRANSMEMBRANE PROTEASE SERINE 13; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 326-586; COMPND 13 SYNONYM: MEMBRANE-TYPE MOSAIC SERINE PROTEASE,MOSAIC SERINE PROTEASE; COMPND 14 EC: 3.4.21.-; COMPND 15 ENGINEERED: YES; COMPND 16 OTHER_DETAILS: CATALYTIC CHAIN; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: DECANOYL-ARG-VAL-LYS-ARG-CHLOROMETHYLKETONE INHIBITOR; COMPND 19 CHAIN: C; COMPND 20 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: TMPRSS13, MSP, TMPRSS11; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: ECV304-MSPLDTM; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: TMPRSS13, MSP, TMPRSS11; SOURCE 14 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: ECV304-MSPLDTM; SOURCE 17 MOL_ID: 3; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS HYDROLASE, STRUCTURAL PROTEIN-INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.OHNO,N.MAITA,Y.OKUMURA,T.NIKAWA REVDAT 6 22-NOV-23 6KD5 1 REMARK REVDAT 5 14-APR-21 6KD5 1 JRNL REVDAT 4 25-NOV-20 6KD5 1 TITLE COMPND JRNL REMARK REVDAT 4 2 1 DBREF SEQADV HETSYN HELIX REVDAT 4 3 1 SHEET SSBOND LINK ATOM REVDAT 3 29-JUL-20 6KD5 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 01-JUL-20 6KD5 1 JRNL REVDAT 1 24-JUN-20 6KD5 0 JRNL AUTH A.OHNO,N.MAITA,T.TABATA,H.NAGANO,K.ARITA,M.ARIYOSHI, JRNL AUTH 2 T.UCHIDA,R.NAKAO,A.ULLA,K.SUGIURA,K.KISHIMOTO, JRNL AUTH 3 S.TESHIMA-KONDO,Y.OKUMURA,T.NIKAWA JRNL TITL CRYSTAL STRUCTURE OF INHIBITOR-BOUND HUMAN MSPL THAT CAN JRNL TITL 2 ACTIVATE HIGH PATHOGENIC AVIAN INFLUENZA. JRNL REF LIFE SCI ALLIANCE V. 4 2021 JRNL REFN ESSN 2575-1077 JRNL PMID 33820827 JRNL DOI 10.26508/LSA.202000849 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 17570 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1493 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) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1258 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.3340 REMARK 3 BIN FREE R VALUE SET COUNT : 108 REMARK 3 BIN FREE R VALUE : 0.4140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2961 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 88 REMARK 3 SOLVENT ATOMS : 81 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.63000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : -2.58000 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): 0.388 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.266 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.194 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.564 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3125 ; 0.004 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2758 ; 0.000 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4247 ; 1.191 ; 1.673 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6416 ; 1.121 ; 1.618 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 369 ; 9.707 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 158 ;34.441 ;21.835 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 506 ;22.088 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;20.214 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 409 ; 0.046 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3416 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 675 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1486 ; 3.676 ; 3.241 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1486 ; 3.676 ; 3.241 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1851 ; 5.562 ; 4.857 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1852 ; 5.561 ; 4.856 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1639 ; 4.571 ; 3.813 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1612 ; 4.518 ; 3.776 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2355 ; 6.848 ; 5.448 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 12215 ; 9.932 ;60.613 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 12201 ; 9.930 ;60.636 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK 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 THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6KD5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012696. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-FEB-13 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19249 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.200 REMARK 200 R MERGE (I) : 0.15100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 1.01200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 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: 2ANY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES(PH7.5), 2.4M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, TEMPERATURE 288K 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 27.92000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 85.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 85.81500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.92000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.20000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 170 REMARK 465 TYR A 171 REMARK 465 LYS A 172 REMARK 465 ASP A 173 REMARK 465 HIS A 174 REMARK 465 ASP A 175 REMARK 465 GLY A 176 REMARK 465 ASP A 177 REMARK 465 TYR A 178 REMARK 465 LYS A 179 REMARK 465 ASP A 180 REMARK 465 HIS A 181 REMARK 465 ASP A 182 REMARK 465 ILE A 183 REMARK 465 ASP A 184 REMARK 465 TYR A 185 REMARK 465 LYS A 186 REMARK 465 ASP A 187 REMARK 465 ASP A 188 REMARK 465 ASP A 189 REMARK 465 ASP A 190 REMARK 465 LYS A 191 REMARK 465 HIS A 192 REMARK 465 GLY A 324 REMARK 465 ARG A 325 REMARK 465 GLN B 564 REMARK 465 GLN B 565 REMARK 465 ASP B 566 REMARK 465 THR B 567 REMARK 465 ALA B 568 REMARK 465 PRO B 569 REMARK 465 SER B 570 REMARK 465 ARG B 571 REMARK 465 LEU B 572 REMARK 465 GLY B 573 REMARK 465 THR B 574 REMARK 465 SER B 575 REMARK 465 SER B 576 REMARK 465 GLY B 577 REMARK 465 GLY B 578 REMARK 465 ASP B 579 REMARK 465 PRO B 580 REMARK 465 GLY B 581 REMARK 465 GLY B 582 REMARK 465 ALA B 583 REMARK 465 PRO B 584 REMARK 465 ARG B 585 REMARK 465 VAL B 586 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 ARG A 201 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER A 242 O3 SO4 A 403 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 OD2 ASP B 408 NH2 ARG B 501 4455 1.98 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 TYR A 197 -97.75 -129.72 REMARK 500 CYS A 211 34.76 75.03 REMARK 500 HIS A 272 -60.40 -97.75 REMARK 500 ASP A 281 65.08 -111.46 REMARK 500 SER A 293 -73.34 71.89 REMARK 500 SER B 335 -2.81 88.17 REMARK 500 ALA B 394 124.74 -37.27 REMARK 500 SER B 427 -177.30 -170.95 REMARK 500 VAL B 485 -93.92 -119.09 REMARK 500 SER B 488 48.46 39.09 REMARK 500 GLN B 508 128.73 -37.24 REMARK 500 LYS B 540 64.28 -151.49 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 514 LEU B 515 149.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 404 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 209 O REMARK 620 2 ASP A 212 OD1 102.3 REMARK 620 3 VAL A 214 O 174.1 79.2 REMARK 620 4 ASP A 216 OD2 87.6 104.2 86.5 REMARK 620 5 ASP A 222 OD2 94.8 161.2 84.7 84.2 REMARK 620 6 GLU A 223 OE2 102.0 78.1 83.9 169.5 90.7 REMARK 620 N 1 2 3 4 5 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS PROTEIN IS CLEAVED AT BETWEEN ARG320-ILE321, THEN TURNS INTO A REMARK 999 MATURE FORM. DBREF 6KD5 A 192 325 UNP Q9BYE2 TMPSD_HUMAN 192 325 DBREF 6KD5 B 326 586 UNP Q9BYE2 TMPSD_HUMAN 326 586 DBREF 6KD5 C 1 6 PDB 6KD5 6KD5 1 6 SEQADV 6KD5 ASP A 170 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 TYR A 171 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 LYS A 172 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 173 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 HIS A 174 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 175 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 GLY A 176 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 177 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 TYR A 178 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 LYS A 179 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 180 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 HIS A 181 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 182 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ILE A 183 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 184 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 TYR A 185 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 LYS A 186 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 187 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 188 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 189 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 ASP A 190 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 LYS A 191 UNP Q9BYE2 EXPRESSION TAG SEQADV 6KD5 VAL B 586 UNP Q9BYE2 LEU 586 VARIANT SEQRES 1 A 156 ASP TYR LYS ASP HIS ASP GLY ASP TYR LYS ASP HIS ASP SEQRES 2 A 156 ILE ASP TYR LYS ASP ASP ASP ASP LYS HIS THR GLY ILE SEQRES 3 A 156 ARG TYR LYS GLU GLN ARG GLU SER CYS PRO LYS HIS ALA SEQRES 4 A 156 VAL ARG CYS ASP GLY VAL VAL ASP CYS LYS LEU LYS SER SEQRES 5 A 156 ASP GLU LEU GLY CYS VAL ARG PHE ASP TRP ASP LYS SER SEQRES 6 A 156 LEU LEU LYS ILE TYR SER GLY SER SER HIS GLN TRP LEU SEQRES 7 A 156 PRO ILE CYS SER SER ASN TRP ASN ASP SER TYR SER GLU SEQRES 8 A 156 LYS THR CYS GLN GLN LEU GLY PHE GLU SER ALA HIS ARG SEQRES 9 A 156 THR THR GLU VAL ALA HIS ARG ASP PHE ALA ASN SER PHE SEQRES 10 A 156 SER ILE LEU ARG TYR ASN SER THR ILE GLN GLU SER LEU SEQRES 11 A 156 HIS ARG SER GLU CYS PRO SER GLN ARG TYR ILE SER LEU SEQRES 12 A 156 GLN CYS SER HIS CYS GLY LEU ARG ALA MET THR GLY ARG SEQRES 1 B 261 ILE VAL GLY GLY ALA LEU ALA SER ASP SER LYS TRP PRO SEQRES 2 B 261 TRP GLN VAL SER LEU HIS PHE GLY THR THR HIS ILE CYS SEQRES 3 B 261 GLY GLY THR LEU ILE ASP ALA GLN TRP VAL LEU THR ALA SEQRES 4 B 261 ALA HIS CYS PHE PHE VAL THR ARG GLU LYS VAL LEU GLU SEQRES 5 B 261 GLY TRP LYS VAL TYR ALA GLY THR SER ASN LEU HIS GLN SEQRES 6 B 261 LEU PRO GLU ALA ALA SER ILE ALA GLU ILE ILE ILE ASN SEQRES 7 B 261 SER ASN TYR THR ASP GLU GLU ASP ASP TYR ASP ILE ALA SEQRES 8 B 261 LEU MET ARG LEU SER LYS PRO LEU THR LEU SER ALA HIS SEQRES 9 B 261 ILE HIS PRO ALA CYS LEU PRO MET HIS GLY GLN THR PHE SEQRES 10 B 261 SER LEU ASN GLU THR CYS TRP ILE THR GLY PHE GLY LYS SEQRES 11 B 261 THR ARG GLU THR ASP ASP LYS THR SER PRO PHE LEU ARG SEQRES 12 B 261 GLU VAL GLN VAL ASN LEU ILE ASP PHE LYS LYS CYS ASN SEQRES 13 B 261 ASP TYR LEU VAL TYR ASP SER TYR LEU THR PRO ARG MET SEQRES 14 B 261 MET CYS ALA GLY ASP LEU ARG GLY GLY ARG ASP SER CYS SEQRES 15 B 261 GLN GLY ASP SER GLY GLY PRO LEU VAL CYS GLU GLN ASN SEQRES 16 B 261 ASN ARG TRP TYR LEU ALA GLY VAL THR SER TRP GLY THR SEQRES 17 B 261 GLY CYS GLY GLN ARG ASN LYS PRO GLY VAL TYR THR LYS SEQRES 18 B 261 VAL THR GLU VAL LEU PRO TRP ILE TYR SER LYS MET GLU SEQRES 19 B 261 VAL ARG SER LEU GLN GLN ASP THR ALA PRO SER ARG LEU SEQRES 20 B 261 GLY THR SER SER GLY GLY ASP PRO GLY GLY ALA PRO ARG SEQRES 21 B 261 VAL SEQRES 1 C 6 DKA ARG VAL LYS AR7 0QE HET DKA C 1 11 HET AR7 C 5 11 HET 0QE C 6 1 HET NAG D 1 14 HET FUC D 2 10 HET NAG E 1 14 HET NAG E 2 14 HET SO4 A 401 5 HET SO4 A 402 5 HET SO4 A 403 5 HET CA A 404 1 HET SO4 B 601 5 HET SO4 B 602 5 HET SO4 B 603 5 HET SO4 C 101 5 HETNAM DKA DECANOIC ACID HETNAM AR7 AMINO{[(4S)-4-AMINO-5,5- HETNAM 2 AR7 DIHYDROXYPENTYL]AMINO}METHANIMINIUM HETNAM 0QE CHLOROMETHANE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM CA CALCIUM ION HETSYN 0QE CHLORO METHYL GROUP HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 3 DKA C10 H20 O2 FORMUL 3 AR7 C6 H17 N4 O2 1+ FORMUL 3 0QE C H3 CL FORMUL 4 NAG 3(C8 H15 N O6) FORMUL 4 FUC C6 H12 O5 FORMUL 6 SO4 7(O4 S 2-) FORMUL 9 CA CA 2+ FORMUL 14 HOH *81(H2 O) HELIX 1 AA1 LYS A 220 LEU A 224 5 5 HELIX 2 AA2 ASP A 256 LEU A 266 1 11 HELIX 3 AA3 ALA B 365 VAL B 370 5 6 HELIX 4 AA4 ASP B 476 ASN B 481 1 6 HELIX 5 AA5 VAL B 550 ARG B 561 1 12 SHEET 1 AA1 7 GLY A 194 ARG A 196 0 SHEET 2 AA1 7 ILE B 397 ILE B 402 1 O ILE B 402 N ARG A 196 SHEET 3 AA1 7 ALA B 416 LEU B 420 -1 O LEU B 417 N ILE B 401 SHEET 4 AA1 7 TRP B 360 THR B 363 -1 N VAL B 361 O MET B 418 SHEET 5 AA1 7 THR B 348 ASP B 357 -1 N THR B 354 O LEU B 362 SHEET 6 AA1 7 GLN B 340 PHE B 345 -1 N LEU B 343 O CYS B 351 SHEET 7 AA1 7 TRP B 379 ALA B 383 -1 O LYS B 380 N HIS B 344 SHEET 1 AA2 3 VAL A 227 ASP A 230 0 SHEET 2 AA2 3 LEU A 235 SER A 240 -1 O LEU A 235 N ASP A 230 SHEET 3 AA2 3 GLN A 245 LEU A 247 -1 O GLN A 245 N SER A 240 SHEET 1 AA3 2 ARG A 273 ALA A 278 0 SHEET 2 AA3 2 ARG A 308 GLN A 313 -1 O TYR A 309 N VAL A 277 SHEET 1 AA4 2 SER A 285 ILE A 288 0 SHEET 2 AA4 2 LEU A 299 SER A 302 -1 O HIS A 300 N SER A 287 SHEET 1 AA5 8 ALA B 330 LEU B 331 0 SHEET 2 AA5 8 ARG B 468 ILE B 475 -1 O GLU B 469 N ALA B 330 SHEET 3 AA5 8 MET B 494 GLY B 498 -1 O CYS B 496 N ILE B 475 SHEET 4 AA5 8 GLY B 542 LYS B 546 -1 O TYR B 544 N MET B 495 SHEET 5 AA5 8 ARG B 522 TRP B 531 -1 N TRP B 531 O VAL B 543 SHEET 6 AA5 8 PRO B 514 GLN B 519 -1 N LEU B 515 O GLY B 527 SHEET 7 AA5 8 THR B 447 GLY B 452 -1 N TRP B 449 O VAL B 516 SHEET 8 AA5 8 ARG B 468 ILE B 475 -1 O VAL B 472 N CYS B 448 SSBOND 1 CYS A 204 CYS A 217 1555 1555 2.04 SSBOND 2 CYS A 211 CYS A 226 1555 1555 2.04 SSBOND 3 CYS A 250 CYS A 304 1555 1555 2.07 SSBOND 4 CYS A 263 CYS A 314 1555 1555 2.05 SSBOND 5 CYS A 317 CYS B 434 1555 1555 2.06 SSBOND 6 CYS B 351 CYS B 367 1555 1555 2.02 SSBOND 7 CYS B 448 CYS B 517 1555 1555 2.05 SSBOND 8 CYS B 480 CYS B 496 1555 1555 2.03 SSBOND 9 CYS B 507 CYS B 535 1555 1555 2.06 LINK ND2 ASN A 255 C1 NAG D 1 1555 1555 1.44 LINK NE2 HIS B 366 C1 0QE C 6 1555 1555 1.28 LINK ND2 ASN B 405 C1 NAG E 1 1555 1555 1.43 LINK OG SER B 511 C AR7 C 5 1555 1555 1.42 LINK C1 DKA C 1 N ARG C 2 1555 1555 1.33 LINK C LYS C 4 N AR7 C 5 1555 1555 1.38 LINK C AR7 C 5 C1 0QE C 6 1555 1555 1.54 LINK O6 NAG D 1 C1 FUC D 2 1555 1555 1.43 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O VAL A 209 CA CA A 404 1555 1555 2.36 LINK OD1 ASP A 212 CA CA A 404 1555 1555 2.49 LINK O VAL A 214 CA CA A 404 1555 1555 2.38 LINK OD2 ASP A 216 CA CA A 404 1555 1555 2.49 LINK OD2 ASP A 222 CA CA A 404 1555 1555 2.30 LINK OE2 GLU A 223 CA CA A 404 1555 1555 2.37 CISPEP 1 TRP A 231 ASP A 232 0 16.64 CRYST1 55.840 62.400 171.630 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 0.017908 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005826 0.00000