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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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