HEADER HYDROLASE/HYDROLASE INHIBITOR 13-SEP-13 4MPU
TITLE HUMAN BETA-TRYPTASE CO-CRYSTAL STRUCTURE WITH (6S,8R)-N,N'-BIS[3-({4-
TITLE 2 [3-(AMINOMETHYL)PHENYL]PIPERIDIN-1-YL}CARBONYL)PHENYL]-8-HYDROXY-6-
TITLE 3 (1-HYDROXYCYCLOBUTYL)-5,7-DIOXASPIRO[3.4]OCTANE-6,8-DICARBOXAMIDE
CAVEAT 4MPU CONFORMATIONS C AND D OF LIGAND X2A HAVE INCORRECT
CAVEAT 2 4MPU STEREOCHEMISTRY AT THEIR C AND C22 CHIRAL CENTERS.
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: TRYPTASE ALPHA/BETA-1;
COMPND 3 CHAIN: A, B;
COMPND 4 FRAGMENT: UNP RESIDUES 31-275;
COMPND 5 SYNONYM: TRYPTASE-1, TRYPTASE I, TRYPTASE ALPHA-1;
COMPND 6 EC: 3.4.21.59;
COMPND 7 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: TPS1, TPS2, TPSAB1, TPSB1;
SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS;
SOURCE 7 EXPRESSION_SYSTEM_COMMON: PICHIA PASTORIS;
SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4922
KEYWDS COFERON, ALPHA-HYDROXYKETONE, SMALL MOLECULE INHIBITOR, DRUG
KEYWDS 2 DISCOVERY, SELF-ASSEMBLY, CRYSTAL CATALYSIS, HYDROLASE-HYDROLASE
KEYWDS 3 INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.WHITE,A.J.STEIN,R.K.SUTO
REVDAT 2 25-SEP-19 4MPU 1 JRNL
REVDAT 1 18-MAR-15 4MPU 0
JRNL AUTH S.F.GIARDINA,D.S.WERNER,M.PINGLE,K.W.FOREMAN,D.E.BERGSTROM,
JRNL AUTH 2 L.D.ARNOLD,F.BARANY
JRNL TITL TARGET-DIRECTED SELF-ASSEMBLY OF HOMODIMERIC DRUGS AGAINST
JRNL TITL 2 BETA-TRYPTASE.
JRNL REF ACS MED.CHEM.LETT. V. 9 827 2018
JRNL REFN ISSN 1948-5875
JRNL PMID 30128075
JRNL DOI 10.1021/ACSMEDCHEMLETT.8B00204
REMARK 2
REMARK 2 RESOLUTION. 1.65 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC 5.7.0029
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.65
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.80
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3
REMARK 3 NUMBER OF REFLECTIONS : 67095
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) : 0.180
REMARK 3 R VALUE (WORKING SET) : 0.178
REMARK 3 FREE R VALUE : 0.216
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 3575
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) : 1.65
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69
REMARK 3 REFLECTION IN BIN (WORKING SET) : 4911
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.42
REMARK 3 BIN R VALUE (WORKING SET) : 0.2620
REMARK 3 BIN FREE R VALUE SET COUNT : 243
REMARK 3 BIN FREE R VALUE : 0.2920
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 3832
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 134
REMARK 3 SOLVENT ATOMS : 515
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.98
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : -0.01000
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): 0.095
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.097
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4458 ; 0.024 ; 0.019
REMARK 3 BOND LENGTHS OTHERS (A): 4090 ; 0.001 ; 0.020
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6161 ; 2.900 ; 2.026
REMARK 3 BOND ANGLES OTHERS (DEGREES): 9420 ; 3.646 ; 3.003
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 514 ; 6.799 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;31.130 ;23.316
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 617 ;14.060 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 27 ;13.332 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 627 ; 0.149 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4982 ; 0.016 ; 0.021
REMARK 3 GENERAL PLANES OTHERS (A): 1071 ; 0.046 ; 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): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
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: NULL
REMARK 4
REMARK 4 4MPU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-SEP-13.
REMARK 100 THE DEPOSITION ID IS D_1000082215.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 25-FEB-11
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : NSLS
REMARK 200 BEAMLINE : X29A
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.075
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : MIRRORS
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70669
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.649
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8
REMARK 200 DATA REDUNDANCY : 4.200
REMARK 200 R MERGE (I) : 0.06800
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.0000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> 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: MOLREP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 53.52
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG1500, 0.1 M SODIUM ACETATE, PH
REMARK 280 4.6, 0.2 M AMMONIUM SULFATE, INDIVIDUAL MONOCRYSTALS
REMARK 280 EQUILIBRATED WITH 30% PEG1500, 0.1 M MES, PH 5.5, 0.2 M AMMONIUM
REMARK 280 SULFATE AND SOAKED 20 HOURS IN SAME SOLUTION SUPPLEMENTED WITH
REMARK 280 COMPOUND 2A, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
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 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.01300
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 110.02600
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 110.02600
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 55.01300
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 11990 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 38110 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -127.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 55.01300
REMARK 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 5080 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 19970 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B
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 LYS A 274
REMARK 465 PRO A 275
REMARK 465 LYS B 274
REMARK 465 PRO B 275
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 B 132 CG CD CE NZ
REMARK 470 LYS B 273 CG CD CE NZ
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 NZ LYS B 81 O HOH B 516 2.02
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 PHE A 58 CB - CG - CD1 ANGL. DEV. = 4.3 DEGREES
REMARK 500 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ARG A 87 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES
REMARK 500 ASP A 162 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES
REMARK 500 ARG A 253 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 ASP B 82 CB - CG - OD2 ANGL. DEV. = -6.2 DEGREES
REMARK 500 ASP B 162 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
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 TRP A 42 54.95 71.01
REMARK 500 ARG A 91 119.38 -39.79
REMARK 500 TYR A 96 -21.36 80.93
REMARK 500 TYR A 114 -48.81 -130.89
REMARK 500 PHE A 149 70.50 54.07
REMARK 500 SER A 243 -59.20 -122.60
REMARK 500 TYR B 96 -15.85 75.73
REMARK 500 TYR B 114 -44.86 -133.76
REMARK 500 SER B 243 -60.65 -124.38
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 A 272 LYS A 273 146.55
REMARK 500
REMARK 500 REMARK: NULL
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES A 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 A 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE X2A B 301
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC5
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MES B 302
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC6
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 303
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC7
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 304
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC8
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 305
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC9
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 B 306
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4MPV RELATED DB: PDB
REMARK 900 RELATED ID: 4MPW RELATED DB: PDB
REMARK 900 RELATED ID: 4MPX RELATED DB: PDB
REMARK 900 RELATED ID: 4MQA RELATED DB: PDB
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 N132K IS A NATURAL VARIANT.
DBREF 4MPU A 31 275 UNP Q15661 TRYB1_HUMAN 31 275
DBREF 4MPU B 31 275 UNP Q15661 TRYB1_HUMAN 31 275
SEQADV 4MPU LYS A 132 UNP Q15661 ASN 132 SEE REMARK 999
SEQADV 4MPU LYS B 132 UNP Q15661 ASN 132 SEE REMARK 999
SEQRES 1 A 245 ILE VAL GLY GLY GLN GLU ALA PRO ARG SER LYS TRP PRO
SEQRES 2 A 245 TRP GLN VAL SER LEU ARG VAL HIS GLY PRO TYR TRP MET
SEQRES 3 A 245 HIS PHE CYS GLY GLY SER LEU ILE HIS PRO GLN TRP VAL
SEQRES 4 A 245 LEU THR ALA ALA HIS CYS VAL GLY PRO ASP VAL LYS ASP
SEQRES 5 A 245 LEU ALA ALA LEU ARG VAL GLN LEU ARG GLU GLN HIS LEU
SEQRES 6 A 245 TYR TYR GLN ASP GLN LEU LEU PRO VAL SER ARG ILE ILE
SEQRES 7 A 245 VAL HIS PRO GLN PHE TYR THR ALA GLN ILE GLY ALA ASP
SEQRES 8 A 245 ILE ALA LEU LEU GLU LEU GLU GLU PRO VAL LYS VAL SER
SEQRES 9 A 245 SER HIS VAL HIS THR VAL THR LEU PRO PRO ALA SER GLU
SEQRES 10 A 245 THR PHE PRO PRO GLY MET PRO CYS TRP VAL THR GLY TRP
SEQRES 11 A 245 GLY ASP VAL ASP ASN ASP GLU ARG LEU PRO PRO PRO PHE
SEQRES 12 A 245 PRO LEU LYS GLN VAL LYS VAL PRO ILE MET GLU ASN HIS
SEQRES 13 A 245 ILE CYS ASP ALA LYS TYR HIS LEU GLY ALA TYR THR GLY
SEQRES 14 A 245 ASP ASP VAL ARG ILE VAL ARG ASP ASP MET LEU CYS ALA
SEQRES 15 A 245 GLY ASN THR ARG ARG ASP SER CYS GLN GLY ASP SER GLY
SEQRES 16 A 245 GLY PRO LEU VAL CYS LYS VAL ASN GLY THR TRP LEU GLN
SEQRES 17 A 245 ALA GLY VAL VAL SER TRP GLY GLU GLY CYS ALA GLN PRO
SEQRES 18 A 245 ASN ARG PRO GLY ILE TYR THR ARG VAL THR TYR TYR LEU
SEQRES 19 A 245 ASP TRP ILE HIS HIS TYR VAL PRO LYS LYS PRO
SEQRES 1 B 245 ILE VAL GLY GLY GLN GLU ALA PRO ARG SER LYS TRP PRO
SEQRES 2 B 245 TRP GLN VAL SER LEU ARG VAL HIS GLY PRO TYR TRP MET
SEQRES 3 B 245 HIS PHE CYS GLY GLY SER LEU ILE HIS PRO GLN TRP VAL
SEQRES 4 B 245 LEU THR ALA ALA HIS CYS VAL GLY PRO ASP VAL LYS ASP
SEQRES 5 B 245 LEU ALA ALA LEU ARG VAL GLN LEU ARG GLU GLN HIS LEU
SEQRES 6 B 245 TYR TYR GLN ASP GLN LEU LEU PRO VAL SER ARG ILE ILE
SEQRES 7 B 245 VAL HIS PRO GLN PHE TYR THR ALA GLN ILE GLY ALA ASP
SEQRES 8 B 245 ILE ALA LEU LEU GLU LEU GLU GLU PRO VAL LYS VAL SER
SEQRES 9 B 245 SER HIS VAL HIS THR VAL THR LEU PRO PRO ALA SER GLU
SEQRES 10 B 245 THR PHE PRO PRO GLY MET PRO CYS TRP VAL THR GLY TRP
SEQRES 11 B 245 GLY ASP VAL ASP ASN ASP GLU ARG LEU PRO PRO PRO PHE
SEQRES 12 B 245 PRO LEU LYS GLN VAL LYS VAL PRO ILE MET GLU ASN HIS
SEQRES 13 B 245 ILE CYS ASP ALA LYS TYR HIS LEU GLY ALA TYR THR GLY
SEQRES 14 B 245 ASP ASP VAL ARG ILE VAL ARG ASP ASP MET LEU CYS ALA
SEQRES 15 B 245 GLY ASN THR ARG ARG ASP SER CYS GLN GLY ASP SER GLY
SEQRES 16 B 245 GLY PRO LEU VAL CYS LYS VAL ASN GLY THR TRP LEU GLN
SEQRES 17 B 245 ALA GLY VAL VAL SER TRP GLY GLU GLY CYS ALA GLN PRO
SEQRES 18 B 245 ASN ARG PRO GLY ILE TYR THR ARG VAL THR TYR TYR LEU
SEQRES 19 B 245 ASP TRP ILE HIS HIS TYR VAL PRO LYS LYS PRO
HET MES A 301 12
HET SO4 A 302 5
HET PG4 A 303 13
HET X2A B 301 256
HET MES B 302 12
HET SO4 B 303 5
HET SO4 B 304 5
HET SO4 B 305 5
HET PG4 B 306 13
HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID
HETNAM SO4 SULFATE ION
HETNAM PG4 TETRAETHYLENE GLYCOL
HETNAM X2A (6S,8R)-N,N'-BIS[3-({4-[3-(AMINOMETHYL)
HETNAM 2 X2A PHENYL]PIPERIDIN-1-YL}CARBONYL)PHENYL]-8-HYDROXY-6-(1-
HETNAM 3 X2A HYDROXYCYCLOBUTYL)-5,7-DIOXASPIRO[3.4]OCTANE-6,8-
HETNAM 4 X2A DICARBOXAMIDE
FORMUL 3 MES 2(C6 H13 N O4 S)
FORMUL 4 SO4 4(O4 S 2-)
FORMUL 5 PG4 2(C8 H18 O5)
FORMUL 6 X2A C50 H58 N6 O8
FORMUL 12 HOH *515(H2 O)
HELIX 1 1 ALA A 72 GLY A 77 1 6
HELIX 2 2 ASP A 82 ALA A 84 5 3
HELIX 3 3 GLU A 184 LEU A 194 1 11
HELIX 4 4 TYR A 263 HIS A 269 1 7
HELIX 5 5 ALA B 72 GLY B 77 1 6
HELIX 6 6 ASP B 82 ALA B 84 5 3
HELIX 7 7 GLU B 184 LEU B 194 1 11
HELIX 8 8 TYR B 263 HIS B 269 1 7
SHEET 1 A 8 GLN A 35 GLU A 36 0
SHEET 2 A 8 LYS A 176 LYS A 179 -1 O GLN A 177 N GLN A 35
SHEET 3 A 8 CYS A 155 GLY A 159 -1 N VAL A 157 O VAL A 178
SHEET 4 A 8 PRO A 227 VAL A 232 -1 O VAL A 229 N TRP A 156
SHEET 5 A 8 THR A 235 TRP A 244 -1 O LEU A 237 N CYS A 230
SHEET 6 A 8 GLY A 255 ARG A 259 -1 O ILE A 256 N TRP A 244
SHEET 7 A 8 MET A 209 ALA A 212 -1 N LEU A 210 O TYR A 257
SHEET 8 A 8 ILE A 182 MET A 183 -1 N MET A 183 O CYS A 211
SHEET 1 B 7 GLN A 45 VAL A 50 0
SHEET 2 B 7 MET A 56 HIS A 65 -1 O CYS A 59 N LEU A 48
SHEET 3 B 7 TRP A 68 THR A 71 -1 O LEU A 70 N SER A 62
SHEET 4 B 7 ALA A 123 LEU A 127 -1 O LEU A 125 N VAL A 69
SHEET 5 B 7 LEU A 102 VAL A 109 -1 N ILE A 108 O LEU A 124
SHEET 6 B 7 LEU A 86 GLN A 89 -1 N VAL A 88 O LEU A 102
SHEET 7 B 7 GLN A 45 VAL A 50 -1 N ARG A 49 O ARG A 87
SHEET 1 C 8 GLN B 35 GLU B 36 0
SHEET 2 C 8 LYS B 176 MET B 183 -1 O GLN B 177 N GLN B 35
SHEET 3 C 8 MET B 209 ALA B 212 -1 O CYS B 211 N MET B 183
SHEET 4 C 8 GLY B 255 ARG B 259 -1 O TYR B 257 N LEU B 210
SHEET 5 C 8 THR B 235 TRP B 244 -1 N TRP B 244 O ILE B 256
SHEET 6 C 8 PRO B 227 VAL B 232 -1 N CYS B 230 O LEU B 237
SHEET 7 C 8 PRO B 154 GLY B 159 -1 N TRP B 156 O VAL B 229
SHEET 8 C 8 LYS B 176 MET B 183 -1 O VAL B 178 N VAL B 157
SHEET 1 D 7 GLN B 45 VAL B 50 0
SHEET 2 D 7 MET B 56 HIS B 65 -1 O CYS B 59 N LEU B 48
SHEET 3 D 7 TRP B 68 THR B 71 -1 O LEU B 70 N SER B 62
SHEET 4 D 7 ALA B 123 LEU B 127 -1 O LEU B 125 N VAL B 69
SHEET 5 D 7 LEU B 102 VAL B 109 -1 N SER B 105 O GLU B 126
SHEET 6 D 7 LEU B 86 GLN B 89 -1 N VAL B 88 O LEU B 102
SHEET 7 D 7 GLN B 45 VAL B 50 -1 N ARG B 49 O ARG B 87
SSBOND 1 CYS A 59 CYS A 75 1555 1555 2.08
SSBOND 2 CYS A 155 CYS A 230 1555 1555 2.01
SSBOND 3 CYS A 188 CYS A 211 1555 1555 2.06
SSBOND 4 CYS A 220 CYS A 248 1555 1555 2.15
SSBOND 5 CYS B 59 CYS B 75 1555 1555 2.12
SSBOND 6 CYS B 155 CYS B 230 1555 1555 2.00
SSBOND 7 CYS B 188 CYS B 211 1555 1555 2.05
SSBOND 8 CYS B 220 CYS B 248 1555 1555 2.07
CISPEP 1 GLY A 77 PRO A 78 0 1.14
CISPEP 2 PRO A 171 PRO A 172 0 8.76
CISPEP 3 GLY B 77 PRO B 78 0 9.72
CISPEP 4 PRO B 171 PRO B 172 0 5.73
SITE 1 AC1 15 PRO A 103 GLN A 112 ILE A 118 GLY A 119
SITE 2 AC1 15 ASP A 207 ASP A 208 TYR A 262 TYR A 263
SITE 3 AC1 15 HOH A 430 HOH A 431 HOH A 471 HOH A 507
SITE 4 AC1 15 HOH A 521 HOH A 637 HOH A 646
SITE 1 AC2 4 HIS A 74 GLN A 221 GLY A 222 SER A 224
SITE 1 AC3 8 VAL A 50 PHE A 58 VAL A 80 LYS A 81
SITE 2 AC3 8 ASP A 82 ALA A 85 HOH A 517 HOH A 525
SITE 1 AC4 24 THR A 115 GLN A 117 ASP A 218 SER A 219
SITE 2 AC4 24 CYS A 220 GLN A 221 SER A 224 TRP A 244
SITE 3 AC4 24 GLY A 245 GLU A 246 GLY A 247 HOH A 424
SITE 4 AC4 24 HOH A 532 GLN B 117 ASP B 218 SER B 219
SITE 5 AC4 24 CYS B 220 SER B 224 TRP B 244 GLY B 245
SITE 6 AC4 24 GLU B 246 GLY B 247 HOH B 432 HOH B 513
SITE 1 AC5 9 LYS A 132 SER A 134 HIS A 136 HOH A 417
SITE 2 AC5 9 ARG B 203 ARG B 206 ASP B 207 SO4 B 305
SITE 3 AC5 9 HOH B 474
SITE 1 AC6 5 ASN B 214 THR B 215 ARG B 216 HOH B 556
SITE 2 AC6 5 HOH B 624
SITE 1 AC7 6 HIS B 74 GLN B 221 GLY B 222 SER B 224
SITE 2 AC7 6 HOH B 555 HOH B 604
SITE 1 AC8 6 HIS A 136 HIS B 186 ARG B 203 MES B 302
SITE 2 AC8 6 HOH B 426 HOH B 537
SITE 1 AC9 6 VAL B 50 LYS B 81 ASP B 82 ALA B 85
SITE 2 AC9 6 HOH B 484 HOH B 572
CRYST1 78.157 78.157 165.039 90.00 90.00 120.00 P 31 2 1 12
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 0.012795 0.007387 0.000000 0.00000
SCALE2 0.000000 0.014774 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006059 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
