HEADER HYDROLASE/HYDROLASE INHIBITOR 18-JUN-13 2M9Q
TITLE NMR STRUCTURE OF AN INHIBITOR BOUND DENGUE NS3 PROTEASE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: SERINE PROTEASE SUBUNIT NS2B, SERINE PROTEASE NS3;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: UNP RESIDUES 1391-1440 AND 1476-1648;
COMPND 5 SYNONYM: FLAVIVIRIN PROTEASE NS2B REGULATORY SUBUNIT, NON-STRUCTURAL
COMPND 6 PROTEIN 2B;
COMPND 7 EC: 3.4.21.91, 3.6.1.15, 3.6.4.13;
COMPND 8 ENGINEERED: YES;
COMPND 9 MOL_ID: 2;
COMPND 10 MOLECULE: SERINE PROTEASE INHIBITOR;
COMPND 11 CHAIN: B;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 2;
SOURCE 3 ORGANISM_TAXID: 413041;
SOURCE 4 STRAIN: THAILAND/0168/1979;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET11A;
SOURCE 8 MOL_ID: 2;
SOURCE 9 SYNTHETIC: YES
KEYWDS NS2B COFACTOR, COVALENT LIGAND, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA SOLUTION NMR
NUMMDL 10
AUTHOR A.GIBBS,R.STEELE,B.TOUNGE
REVDAT 3 15-NOV-23 2M9Q 1 LINK ATOM
REVDAT 2 14-JUN-23 2M9Q 1 REMARK LINK
REVDAT 1 09-JUL-14 2M9Q 0
JRNL AUTH A.GIBBS,R.STEELE,B.TOUNGE
JRNL TITL NMR STRUCTURE OF AN INHIBITOR BOUND DENGUE NS3 PROTEASE
JRNL TITL 2 PROVIDES NEW INSIGHTS INTO THE NS2B NS3 LIGAND INTERACTIONS
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2M9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JUL-13.
REMARK 100 THE DEPOSITION ID IS D_1000103386.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.5
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-13C; U-15N; U-2H]
REMARK 210 PROTEIN, 0.8 MM [U-5% 13C; U-100%
REMARK 210 15N] PROTEIN, 0.8 MM [U-13C; U-
REMARK 210 15N; U-2H];[1H-13C]-I(DELTA1)LVM
REMARK 210 PROTEIN, 95% H2O/5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HN(CA)CO; 3D
REMARK 210 HNCO; 3D CBCA(CO)NH; 3D HNCACB;
REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY;
REMARK 210 3D HCCH-TOCSY; 3D CCH-TOCSY; 3D
REMARK 210 CCH-NOESY; 3D CNH-NOESY; 3D NCH-
REMARK 210 NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : X-PLOR, AUTOSTRUCTURE
REMARK 210 METHOD USED : SIMULATED ANNEALING
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST
REMARK 210 ENERGY
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
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: DIMERIC
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 400
REMARK 400 COMPOUND
REMARK 400
REMARK 400 THE SERINE PROTEASE INHIBITOR BEZ-NLE-LYS-ARG-M9P IS PEPTIDE-LIKE,
REMARK 400 A MEMBER OF ENZYME INHIBITOR CLASS.
REMARK 400
REMARK 400 GROUP: 1
REMARK 400 NAME: SERINE PROTEASE INHIBITOR BEZ-NLE-LYS-ARG-M9P
REMARK 400 CHAIN: B
REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER
REMARK 400 DESCRIPTION: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
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
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 1 ASP A 5 90.73 -174.84
REMARK 500 1 ALA A 12 -169.67 -161.06
REMARK 500 1 GLN A 19 36.06 -82.61
REMARK 500 1 SER A 23 -24.37 -144.62
REMARK 500 1 PRO A 27 -96.30 -65.67
REMARK 500 1 ASP A 36 -42.76 75.95
REMARK 500 1 GLU A 46 116.93 -160.81
REMARK 500 1 GLU A 47 41.03 -160.84
REMARK 500 1 LEU A 50 -71.29 -160.29
REMARK 500 1 GLU A 60 -50.51 -175.00
REMARK 500 1 ALA A 62 -60.71 -167.88
REMARK 500 1 VAL A 64 -122.15 -127.84
REMARK 500 1 LEU A 65 142.41 -179.68
REMARK 500 1 ASP A 67 66.72 179.73
REMARK 500 1 VAL A 74 94.67 58.37
REMARK 500 1 LYS A 76 -75.06 64.68
REMARK 500 1 LEU A 79 102.38 -161.99
REMARK 500 1 ASP A 81 101.82 72.39
REMARK 500 1 ILE A 91 -80.02 59.07
REMARK 500 1 GLU A 104 -79.61 65.73
REMARK 500 1 LYS A 122 72.75 1.98
REMARK 500 1 ASP A 136 44.15 79.84
REMARK 500 1 LEU A 146 -91.64 -123.64
REMARK 500 1 GLU A 147 -69.09 167.80
REMARK 500 1 GLU A 152 93.82 -63.03
REMARK 500 1 PRO A 193 103.48 -45.17
REMARK 500 1 VAL A 207 -62.72 68.25
REMARK 500 1 LYS A 231 129.79 68.01
REMARK 500 1 ILE A 233 88.41 -69.26
REMARK 500 1 ILE A 239 -52.51 -152.33
REMARK 500 1 NLE B 252 99.62 50.64
REMARK 500 1 LYS B 253 -85.70 172.02
REMARK 500 1 ARG B 254 -90.12 -102.38
REMARK 500 2 ALA A 4 31.64 -152.17
REMARK 500 2 ASP A 5 61.59 -166.81
REMARK 500 2 ALA A 12 -164.49 -163.67
REMARK 500 2 LYS A 15 117.43 -172.39
REMARK 500 2 GLU A 17 65.71 -158.79
REMARK 500 2 GLN A 19 33.07 -150.59
REMARK 500 2 ALA A 20 73.12 13.65
REMARK 500 2 SER A 23 -51.16 -146.97
REMARK 500 2 SER A 25 34.25 179.88
REMARK 500 2 PRO A 27 178.24 -58.41
REMARK 500 2 ASP A 36 -68.43 72.87
REMARK 500 2 LYS A 42 29.12 49.94
REMARK 500 2 LEU A 65 127.68 81.39
REMARK 500 2 ASP A 67 105.15 175.23
REMARK 500 2 PRO A 73 90.98 -57.14
REMARK 500 2 ALA A 77 -174.55 -175.53
REMARK 500 2 GLU A 80 168.77 50.91
REMARK 500
REMARK 500 THIS ENTRY HAS 365 RAMACHANDRAN OUTLIERS.
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 GLY A 98 ALA A 99 1 -149.80
REMARK 500 LYS A 89 GLY A 90 8 -145.70
REMARK 500 NLE B 252 LYS B 253 8 -148.86
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY
REMARK 500
REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY
REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER
REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 500 I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI ANGLE
REMARK 500 9 ALA A 186 -11.61
REMARK 500 10 ALA A 186 -11.95
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2M9P RELATED DB: PDB
REMARK 900 RELATED ID: 19306 RELATED DB: BMRB
DBREF 2M9Q A 1 240 PDB 2M9Q 2M9Q 1 240
DBREF 2M9Q B 251 255 PDB 2M9Q 2M9Q 251 255
SEQRES 1 A 240 GLY SER ALA ALA ASP LEU GLU LEU GLU ARG ALA ALA ASP
SEQRES 2 A 240 VAL LYS TRP GLU ASP GLN ALA GLU ILE SER GLY SER SER
SEQRES 3 A 240 PRO ILE LEU SER ILE THR ILE SER GLU ASP GLY SER MET
SEQRES 4 A 240 SER ILE LYS ASN GLU GLU GLU GLU GLN THR LEU GLY GLY
SEQRES 5 A 240 GLY GLY SER GLY GLY GLY GLY GLU PHE ALA GLY VAL LEU
SEQRES 6 A 240 TRP ASP VAL PRO SER PRO PRO PRO VAL GLY LYS ALA GLU
SEQRES 7 A 240 LEU GLU ASP GLY ALA TYR ARG ILE LYS GLN LYS GLY ILE
SEQRES 8 A 240 LEU GLY TYR SER GLN ILE GLY ALA GLY VAL TYR LYS GLU
SEQRES 9 A 240 GLY THR PHE HIS THR MET TRP HIS VAL THR ARG GLY ALA
SEQRES 10 A 240 VAL LEU MET HIS LYS GLY LYS ARG ILE GLU PRO SER TRP
SEQRES 11 A 240 ALA ASP VAL LYS LYS ASP LEU ILE SER TYR GLY GLY GLY
SEQRES 12 A 240 TRP LYS LEU GLU GLY GLU TRP LYS GLU GLY GLU GLU VAL
SEQRES 13 A 240 GLN VAL LEU ALA LEU GLU PRO GLY LYS ASN PRO ARG ALA
SEQRES 14 A 240 VAL GLN THR LYS PRO GLY LEU PHE LYS THR ASN ALA GLY
SEQRES 15 A 240 THR ILE GLY ALA VAL SER LEU ASP PHE SER PRO GLY THR
SEQRES 16 A 240 SER GLY SER PRO ILE ILE ASP LYS LYS GLY LYS VAL VAL
SEQRES 17 A 240 GLY LEU TYR GLY ASN GLY VAL VAL THR ARG SER GLY ALA
SEQRES 18 A 240 TYR VAL SER ALA ILE ALA GLN THR GLU LYS SER ILE GLU
SEQRES 19 A 240 ASP ASN PRO GLU ILE GLU
SEQRES 1 B 5 BEZ NLE LYS ARG M9P
MODRES 2M9Q NLE B 252 LEU NORLEUCINE
HET BEZ B 251 13
HET NLE B 252 19
HET M9P B 255 29
HETNAM BEZ BENZOIC ACID
HETNAM NLE NORLEUCINE
HETNAM M9P AMINO{[(4S,5S)-4-AMINO-6,6,6-TRIFLUORO-5-
HETNAM 2 M9P HYDROXYHEXYL]AMINO}METHANIMINIUM
FORMUL 2 BEZ C7 H6 O2
FORMUL 2 NLE C6 H13 N O2
FORMUL 2 M9P C7 H16 F3 N4 O 1+
SHEET 1 A 6 LEU A 6 ALA A 12 0
SHEET 2 A 6 GLY A 82 GLY A 90 -1 O ARG A 85 N GLU A 9
SHEET 3 A 6 GLY A 93 LYS A 103 -1 O SER A 95 N GLN A 88
SHEET 4 A 6 THR A 106 MET A 110 -1 O THR A 106 N LYS A 103
SHEET 5 A 6 LEU A 137 TYR A 140 -1 O ILE A 138 N THR A 109
SHEET 6 A 6 TRP A 130 ASP A 132 -1 N TRP A 130 O SER A 139
SHEET 1 B 4 GLU A 21 ILE A 22 0
SHEET 2 B 4 PRO A 167 THR A 172 1 O ALA A 169 N GLU A 21
SHEET 3 B 4 VAL A 156 LEU A 161 -1 N VAL A 158 O VAL A 170
SHEET 4 B 4 ILE A 200 ILE A 201 -1 O ILE A 201 N GLN A 157
SHEET 1 C 5 ILE A 28 SER A 30 0
SHEET 2 C 5 GLY A 175 THR A 179 1 O LYS A 178 N LEU A 29
SHEET 3 C 5 GLY A 182 LEU A 189 -1 O ILE A 184 N PHE A 177
SHEET 4 C 5 ALA A 221 ALA A 227 -1 O TYR A 222 N LEU A 189
SHEET 5 C 5 LEU A 210 THR A 217 -1 N GLY A 212 O ALA A 225
SHEET 1 D 2 THR A 32 SER A 34 0
SHEET 2 D 2 SER A 38 SER A 40 -1 O SER A 38 N SER A 34
SHEET 1 E 2 LEU A 119 HIS A 121 0
SHEET 2 E 2 LYS A 124 ILE A 126 -1 O ILE A 126 N LEU A 119
LINK OG SER A 196 C M9P B 255 1555 1555 1.46
LINK C BEZ B 251 N NLE B 252 1555 1555 1.36
LINK C NLE B 252 N LYS B 253 1555 1555 1.38
LINK C ARG B 254 N M9P B 255 1555 1555 1.34
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1
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 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END
