HEADER HYDROLASE/HYDROLASE INHIBITOR 04-JAN-11 3Q77 TITLE STRUCTURE OF HUMAN NEUTROPHIL ELASTASE IN COMPLEX WITH A TITLE 2 DIHYDROPYRIMIDONE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEUTROPHIL ELASTASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 30-247; COMPND 5 SYNONYM: BONE MARROW SERINE PROTEASE, ELASTASE-2, HUMAN LEUKOCYTE COMPND 6 ELASTASE, HLE, MEDULLASIN, PMN ELASTASE; COMPND 7 EC: 3.4.21.37 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS TRYPSIN FAMILY FOLD, PROTEASE, HYDROLASE, HYDROLASE-HYDROLASE KEYWDS 2 INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.HANSEN,K.NIEFIND REVDAT 6 13-SEP-23 3Q77 1 HETSYN LINK REVDAT 5 29-JUL-20 3Q77 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 17-JUL-19 3Q77 1 REMARK LINK REVDAT 3 15-JUN-11 3Q77 1 JRNL REVDAT 2 25-MAY-11 3Q77 1 JRNL REVDAT 1 11-MAY-11 3Q77 0 JRNL AUTH G.HANSEN,H.GIELEN-HAERTWIG,P.REINEMER,D.SCHOMBURG, JRNL AUTH 2 A.HARRENGA,K.NIEFIND JRNL TITL UNEXPECTED ACTIVE-SITE FLEXIBILITY IN THE STRUCTURE OF HUMAN JRNL TITL 2 NEUTROPHIL ELASTASE IN COMPLEX WITH A NEW DIHYDROPYRIMIDONE JRNL TITL 3 INHIBITOR. JRNL REF J.MOL.BIOL. V. 409 681 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21549129 JRNL DOI 10.1016/J.JMB.2011.04.047 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.4_486 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 NUMBER OF REFLECTIONS : 14457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 735 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 24.1362 - 3.4132 1.00 2871 153 0.1484 0.1756 REMARK 3 2 3.4132 - 2.7103 1.00 2844 130 0.1544 0.1918 REMARK 3 3 2.7103 - 2.3681 1.00 2806 158 0.1565 0.2234 REMARK 3 4 2.3681 - 2.1517 1.00 2798 158 0.1702 0.2275 REMARK 3 5 2.1517 - 1.9976 0.86 2403 136 0.1963 0.2587 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 46.02 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.42690 REMARK 3 B22 (A**2) : -1.42690 REMARK 3 B33 (A**2) : 2.85380 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 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 : 0.008 1760 REMARK 3 ANGLE : 1.152 2395 REMARK 3 CHIRALITY : 0.074 280 REMARK 3 PLANARITY : 0.004 308 REMARK 3 DIHEDRAL : 20.883 638 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3Q77 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063280. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14498 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.998 REMARK 200 RESOLUTION RANGE LOW (A) : 24.134 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.80 REMARK 200 R MERGE FOR SHELL (I) : 0.35000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1HNE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% W/V PEG3350, 0.2 M AMMONIUM REMARK 280 CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K, PH 5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.32900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 35.32900 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 35.32900 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, 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 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 HIS A 71 -57.37 -137.11 REMARK 500 ASN A 91 50.92 -144.16 REMARK 500 TYR A 94 119.90 -37.96 REMARK 500 LEU A 223 -57.27 -128.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q76 RELATED DB: PDB DBREF 3Q77 A 16 243 UNP P08246 ELNE_HUMAN 30 247 SEQRES 1 A 218 ILE VAL GLY GLY ARG ARG ALA ARG PRO HIS ALA TRP PRO SEQRES 2 A 218 PHE MET VAL SER LEU GLN LEU ARG GLY GLY HIS PHE CYS SEQRES 3 A 218 GLY ALA THR LEU ILE ALA PRO ASN PHE VAL MET SER ALA SEQRES 4 A 218 ALA HIS CYS VAL ALA ASN VAL ASN VAL ARG ALA VAL ARG SEQRES 5 A 218 VAL VAL LEU GLY ALA HIS ASN LEU SER ARG ARG GLU PRO SEQRES 6 A 218 THR ARG GLN VAL PHE ALA VAL GLN ARG ILE PHE GLU ASN SEQRES 7 A 218 GLY TYR ASP PRO VAL ASN LEU LEU ASN ASP ILE VAL ILE SEQRES 8 A 218 LEU GLN LEU ASN GLY SER ALA THR ILE ASN ALA ASN VAL SEQRES 9 A 218 GLN VAL ALA GLN LEU PRO ALA GLN GLY ARG ARG LEU GLY SEQRES 10 A 218 ASN GLY VAL GLN CYS LEU ALA MET GLY TRP GLY LEU LEU SEQRES 11 A 218 GLY ARG ASN ARG GLY ILE ALA SER VAL LEU GLN GLU LEU SEQRES 12 A 218 ASN VAL THR VAL VAL THR SER LEU CYS ARG ARG SER ASN SEQRES 13 A 218 VAL CYS THR LEU VAL ARG GLY ARG GLN ALA GLY VAL CYS SEQRES 14 A 218 PHE GLY ASP SER GLY SER PRO LEU VAL CYS ASN GLY LEU SEQRES 15 A 218 ILE HIS GLY ILE ALA SER PHE VAL ARG GLY GLY CYS ALA SEQRES 16 A 218 SER GLY LEU TYR PRO ASP ALA PHE ALA PRO VAL ALA GLN SEQRES 17 A 218 PHE VAL ASN TRP ILE ASP SER ILE ILE GLN MODRES 3Q77 ASN A 159 ASN GLYCOSYLATION SITE MODRES 3Q77 ASN A 109 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET FUC B 3 10 HET NAG A 411 14 HET 2HY A 500 32 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM 2HY 2-HYDROXYETHYL (4R)-4-(4-CYANOPHENYL)-6-METHYL-2-OXO-1- HETNAM 2 2HY [3-(TRIFLUOROMETHYL)PHENYL]-1,2,3,4- HETNAM 3 2HY TETRAHYDROPYRIMIDINE-5-CARBOXYLATE 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 2 NAG 3(C8 H15 N O6) FORMUL 2 FUC C6 H12 O5 FORMUL 4 2HY C22 H18 F3 N3 O4 FORMUL 5 HOH *136(H2 O) HELIX 1 1 ALA A 55 ALA A 60 1 6 HELIX 2 2 ASN A 62A ALA A 64 5 4 HELIX 3 3 PHE A 234 GLN A 243 1 10 SHEET 1 A 8 ARG A 20 ARG A 21 0 SHEET 2 A 8 GLN A 156 VAL A 164 -1 O GLU A 157 N ARG A 20 SHEET 3 A 8 VAL A 181 LEU A 184 -1 O CYS A 182 N VAL A 164 SHEET 4 A 8 ASP A 226 PRO A 230 -1 O ASP A 226 N THR A 183 SHEET 5 A 8 LEU A 208 PHE A 215 -1 N ILE A 212 O ALA A 229 SHEET 6 A 8 PRO A 198 CYS A 201 -1 N CYS A 201 O LEU A 208 SHEET 7 A 8 GLN A 135 GLY A 140 -1 N LEU A 137 O VAL A 200 SHEET 8 A 8 GLN A 156 VAL A 164 -1 O VAL A 160 N CYS A 136 SHEET 1 B 7 MET A 30 LEU A 35 0 SHEET 2 B 7 GLY A 39 ALA A 48 -1 O GLY A 39 N LEU A 35 SHEET 3 B 7 PHE A 51 SER A 54 -1 O MET A 53 N THR A 45 SHEET 4 B 7 VAL A 104 LEU A 108 -1 O LEU A 106 N VAL A 52 SHEET 5 B 7 GLN A 81 GLU A 90 -1 N GLN A 86 O GLN A 107 SHEET 6 B 7 ARG A 65A LEU A 68 -1 N VAL A 66 O PHE A 83 SHEET 7 B 7 MET A 30 LEU A 35 -1 N GLN A 34 O ARG A 65A SSBOND 1 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 2 CYS A 136 CYS A 201 1555 1555 2.04 SSBOND 3 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 4 CYS A 191 CYS A 220 1555 1555 2.04 LINK ND2 ASN A 109 C1 NAG A 411 1555 1555 1.45 LINK ND2 ASN A 159 C1 NAG B 1 1555 1555 1.42 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK O6 NAG B 1 C1 FUC B 3 1555 1555 1.44 CRYST1 73.732 73.732 70.658 90.00 90.00 120.00 P 63 6 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 0.013563 0.007830 0.000000 0.00000 SCALE2 0.000000 0.015661 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014153 0.00000