HEADER HYDROLASE 24-SEP-99 1B2I TITLE KRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF TITLE 2 TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID (AMCHA) COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (PLASMINOGEN); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: KRINGLE 2 DOMAIN; COMPND 5 EC: 3.4.21.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PQE-8 KEYWDS SERINE PROTEASE, FIBRINOLYSIS, LYSINE-BINDING DOMAIN, PLASMINOGEN, KEYWDS 2 KRINGLE 2, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR D.N.MARTI,J.SCHALLER,M.LLINAS REVDAT 6 27-DEC-23 1B2I 1 REMARK REVDAT 5 03-NOV-21 1B2I 1 REMARK SEQADV REVDAT 4 29-NOV-17 1B2I 1 REMARK HELIX REVDAT 3 24-FEB-09 1B2I 1 VERSN REVDAT 2 01-APR-03 1B2I 1 JRNL REVDAT 1 19-NOV-99 1B2I 0 JRNL AUTH D.N.MARTI,J.SCHALLER,M.LLINAS JRNL TITL SOLUTION STRUCTURE AND DYNAMICS OF THE PLASMINOGEN KRINGLE JRNL TITL 2 2-AMCHA COMPLEX: 3(1)-HELIX IN HOMOLOGOUS DOMAINS. JRNL REF BIOCHEMISTRY V. 38 15741 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10625440 JRNL DOI 10.1021/BI9917378 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.N.MARTI,C.K.HU,S.S.A.AN,P.VON HALLER,J.SCHALLER,M.LLINAS REMARK 1 TITL LIGAND PREFERENCES OF KRINGLE 2 AND HOMOLOGOUS DOMAINS OF REMARK 1 TITL 2 HUMAN PLASMINOGEN: CANVASSING WEAK, INTERMEDIATE AND REMARK 1 TITL 3 HIGH-AFFINITY BINDING SITES BY 1H-NMR REMARK 1 REF BIOCHEMISTRY V. 36 11591 1997 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.SOEHNDEL,C.K.HU,D.MARTI,M.AFFOLTER,J.SCHALLER,M.LLINAS, REMARK 1 AUTH 2 E.E.RICKLI REMARK 1 TITL RECOMBINANT GENE EXPRESSION AND 1H NMR CHARACTERISTICS OF REMARK 1 TITL 2 THE KRINGLE (2+3) SUPERMODULE: SPECTROSCOPIC/FUNCTIONAL REMARK 1 TITL 3 INDIVIDUALITY OF PLASMINOGEN KRINGLE DOMAINS REMARK 1 REF BIOCHEMISTRY V. 35 2357 1996 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 3 REMARK 1 AUTH D.MARTI,J.SCHALLER,B.OCHENSBERGER,E.E.RICKLI REMARK 1 TITL EXPRESSION, PURIFICATION AND CHARACTERIZATION OF THE REMARK 1 TITL 2 RECOMBINANT KRINGLE 2 AND KRINGLE 3 DOMAINS OF HUMAN REMARK 1 TITL 3 PLASMINOGEN AND ANALYSIS OF THEIR BINDING AFFINITY FOR REMARK 1 TITL 4 OMEGA-AMINOCARBOXYLIC ACIDS REMARK 1 REF EUR.J.BIOCHEM. V. 219 455 1994 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CHARMM 23.2 REMARK 3 AUTHORS : BROOKS ET AL., J. COMPUT. CHEM. 4, 187-217 (1983) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B2I COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-DEC-98. REMARK 100 THE DEPOSITION ID IS D_1000000177. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 5.1 REMARK 210 IONIC STRENGTH : SEE PAPER REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY; NOESY; TOCSY; 3D-NOESY REMARK 210 HSQC; 3D-TOCSY HSQC; HNCA; HN(CO) REMARK 210 CA; HCC(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX500; DRX600 REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : DISTANCE GEOMETRY, DYNAMIC REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 150 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TOTAL ENERGY, RAMACHANDRAN PLOT, REMARK 210 LEAST RESTRAINT VIOLATION 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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: 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: 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 4 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A 79 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 5 ARG A 56 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 5 ARG A 59 NE - CZ - NH1 ANGL. DEV. = 3.1 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 1 SER A -3 -64.63 -166.40 REMARK 500 1 TYR A 9 118.47 -36.29 REMARK 500 1 LYS A 12 -11.39 -160.92 REMARK 500 1 SER A 14 45.87 -147.40 REMARK 500 1 ASP A 26 -143.00 -80.16 REMARK 500 1 GLN A 28 -80.98 -149.34 REMARK 500 1 SER A 29 144.63 169.87 REMARK 500 1 ASN A 45 -96.05 -104.43 REMARK 500 1 LYS A 47 -140.22 -157.08 REMARK 500 1 LYS A 48 -96.55 -73.68 REMARK 500 1 LEU A 58 -70.38 -55.86 REMARK 500 1 PRO A 68 -2.94 -57.27 REMARK 500 1 ARG A 71 -88.61 -61.37 REMARK 500 2 GLU A -2 63.83 62.06 REMARK 500 2 GLU A -1 45.13 -75.44 REMARK 500 2 SER A 14 49.22 -143.01 REMARK 500 2 ASP A 26 -141.70 -84.20 REMARK 500 2 GLN A 28 -76.11 -145.81 REMARK 500 2 SER A 29 147.55 179.77 REMARK 500 2 ASN A 45 -79.85 -36.78 REMARK 500 2 LYS A 47 -141.03 -137.19 REMARK 500 2 LYS A 48 -85.11 -68.51 REMARK 500 2 ASN A 49 22.57 -140.83 REMARK 500 2 LEU A 58 -86.93 -63.36 REMARK 500 2 PRO A 68 -7.00 -56.62 REMARK 500 2 ARG A 71 -83.25 -59.47 REMARK 500 3 ASP A 10 54.83 -113.18 REMARK 500 3 LYS A 12 -30.63 -154.15 REMARK 500 3 ASP A 26 -129.02 -75.06 REMARK 500 3 GLN A 28 -65.22 -147.86 REMARK 500 3 LYS A 47 -134.00 -151.27 REMARK 500 3 LYS A 48 -87.18 -66.60 REMARK 500 3 ARG A 56 81.44 33.58 REMARK 500 3 LEU A 58 -72.41 -60.44 REMARK 500 3 PRO A 68 -4.08 -58.06 REMARK 500 3 ARG A 71 -79.43 -54.91 REMARK 500 4 SER A -3 81.17 60.79 REMARK 500 4 ASP A 10 61.95 -164.83 REMARK 500 4 LYS A 12 -8.22 -144.02 REMARK 500 4 ASP A 26 -129.30 -76.50 REMARK 500 4 GLN A 28 -67.17 -146.79 REMARK 500 4 ASN A 45 -93.79 -34.52 REMARK 500 4 LYS A 47 -142.78 -109.95 REMARK 500 4 LYS A 48 -83.45 -61.03 REMARK 500 4 GLU A 57 -163.93 -72.80 REMARK 500 4 LEU A 58 -70.51 -70.25 REMARK 500 4 ARG A 71 -82.86 -53.12 REMARK 500 5 ASP A 10 35.42 -144.05 REMARK 500 5 LYS A 12 -9.70 -145.76 REMARK 500 5 ASP A 26 -144.19 -84.11 REMARK 500 REMARK 500 THIS ENTRY HAS 258 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 4 TYR A 9 0.07 SIDE CHAIN REMARK 500 6 TYR A 9 0.10 SIDE CHAIN REMARK 500 6 ARG A 71 0.07 SIDE CHAIN REMARK 500 7 ARG A 52 0.08 SIDE CHAIN REMARK 500 8 TYR A 9 0.08 SIDE CHAIN REMARK 500 9 ARG A 52 0.10 SIDE CHAIN REMARK 500 12 TYR A 9 0.08 SIDE CHAIN REMARK 500 14 ARG A 71 0.07 SIDE CHAIN REMARK 500 16 TYR A 9 0.08 SIDE CHAIN REMARK 500 18 ARG A 52 0.08 SIDE CHAIN REMARK 500 18 ARG A 56 0.11 SIDE CHAIN REMARK 500 20 TYR A 9 0.08 SIDE CHAIN REMARK 500 20 ARG A 59 0.08 SIDE CHAIN REMARK 500 20 ARG A 79 0.10 SIDE CHAIN 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 AMH A 84 DBREF 1B2I A -4 81 UNP P00747 PLMN_HUMAN 181 263 SEQADV 1B2I THR A -4 UNP P00747 CYS 181 ENGINEERED MUTATION SEQADV 1B2I SER A -3 UNP P00747 GLU 182 ENGINEERED MUTATION SEQADV 1B2I GLY A 4 UNP P00747 CYS 188 ENGINEERED MUTATION SEQRES 1 A 83 THR SER GLU GLU CYS MET HIS GLY SER GLY GLU ASN TYR SEQRES 2 A 83 ASP GLY LYS ILE SER LYS THR MET SER GLY LEU GLU CYS SEQRES 3 A 83 GLN ALA TRP ASP SER GLN SER PRO HIS ALA HIS GLY TYR SEQRES 4 A 83 ILE PRO SER LYS PHE PRO ASN LYS ASN LEU LYS LYS ASN SEQRES 5 A 83 TYR CYS ARG ASN PRO ASP ARG GLU LEU ARG PRO TRP CYS SEQRES 6 A 83 PHE THR THR ASP PRO ASN LYS ARG TRP GLU LEU CYS ASP SEQRES 7 A 83 ILE PRO ARG CYS THR HET AMH A 84 26 HETNAM AMH TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID FORMUL 2 AMH C8 H15 N O2 HELIX 1 H1 GLU A 21 ALA A 24 10POLYPROLINE LIKE 3/1 HELIX 4 HELIX 2 H2 PRO A 38 PHE A 41 5 4 HELIX 3 H3 TYR A 50 CYS A 51 10POLYPROLINE LIKE 3/1 HELIX 2 HELIX 4 H4 ARG A 59 PRO A 61 10POLYPROLINE LIKE 3/1 HELIX 2 HELIX 5 H5 PHE A 64 THR A 65 10POLYPROLINE LIKE 3/1 HELIX 2 HELIX 6 H6 LEU A 74 ARG A 79 10POLYPROLINE LIKE 3/1 HELIX 6 SHEET 1 S1 2 LYS A 15 THR A 16 0 SHEET 2 S1 2 LEU A 20 GLU A 21 -1 O LEU A 20 N THR A 16 SHEET 1 S2 2 ALA A 24 TRP A 25 0 SHEET 2 S2 2 LYS A 48 ASN A 49 -1 O LYS A 48 N TRP A 25 SHEET 1 S3 2 TRP A 62 PHE A 64 0 SHEET 2 S3 2 TRP A 72 LEU A 74 -1 O GLU A 73 N CYS A 63 SSBOND 1 CYS A 1 CYS A 80 1555 1555 2.05 SSBOND 2 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 3 CYS A 51 CYS A 75 1555 1555 2.02 CISPEP 1 SER A 29 PRO A 30 1 10.89 CISPEP 2 SER A 29 PRO A 30 2 12.55 CISPEP 3 SER A 29 PRO A 30 3 -9.85 CISPEP 4 SER A 29 PRO A 30 4 -9.46 CISPEP 5 SER A 29 PRO A 30 5 19.08 CISPEP 6 SER A 29 PRO A 30 6 10.89 CISPEP 7 SER A 29 PRO A 30 7 -8.39 CISPEP 8 SER A 29 PRO A 30 8 -8.21 CISPEP 9 SER A 29 PRO A 30 9 11.11 CISPEP 10 SER A 29 PRO A 30 10 -10.37 CISPEP 11 SER A 29 PRO A 30 11 8.45 CISPEP 12 SER A 29 PRO A 30 12 20.44 CISPEP 13 SER A 29 PRO A 30 13 -13.93 CISPEP 14 SER A 29 PRO A 30 14 -7.63 CISPEP 15 SER A 29 PRO A 30 15 7.64 CISPEP 16 SER A 29 PRO A 30 16 10.86 CISPEP 17 SER A 29 PRO A 30 17 -14.84 CISPEP 18 SER A 29 PRO A 30 18 19.79 CISPEP 19 SER A 29 PRO A 30 19 9.20 CISPEP 20 SER A 29 PRO A 30 20 -22.13 SITE 1 AC1 7 TYR A 36 ASP A 55 GLU A 57 TRP A 62 SITE 2 AC1 7 PHE A 64 ARG A 71 TRP A 72 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