3DA9 - Header Asymmetric Unit

HEADER HYDROLASE 29-MAY-08 3DA9

TITLE CRYSTAL STRUCTURE OF THROMBIN IN COMPLEX WITH INHIBITOR

COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 328-363; COMPND 5 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE COMPND 6 FRAGMENT 1, ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN LIGHT COMPND 7 CHAIN; COMPND 8 EC: 3.4.21.5; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 364-622; COMPND 13 SYNONYM: COAGULATION FACTOR II, ACTIVATION PEPTIDE COMPND 14 FRAGMENT 1, ACTIVATION PEPTIDE FRAGMENT 2, THROMBIN HEAVY COMPND 15 CHAIN; COMPND 16 EC: 3.4.21.5; COMPND 17 MOL_ID: 3; COMPND 18 MOLECULE: HIRUDIN PEPTIDE; COMPND 19 CHAIN: D; 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 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 7 ORGANISM_COMMON: HUMAN; SOURCE 8 ORGANISM_TAXID: 9606; SOURCE 9 MOL_ID: 3; SOURCE 10 SYNTHETIC: YES

KEYWDS THROMBIN, INHIBITOR COMPLEX, ACUTE PHASE, BLOOD COAGULATION, KEYWDS 2 CALCIUM, CLEAVAGE ON PAIR OF BASIC RESIDUES, DISEASE KEYWDS 3 MUTATION, GAMMA-CARBOXYGLUTAMIC ACID, GLYCOPROTEIN, KEYWDS 4 HYDROLASE, KRINGLE, PHARMACEUTICAL, POLYMORPHISM, PROTEASE, KEYWDS 5 SECRETED, SERINE PROTEASE, ZYMOGEN

EXPDTA X-RAY DIFFRACTION

AUTHOR Y.XUE,S.K.HANSSON

REVDAT 1 19-MAY-09 3DA9 0

JRNL AUTH M.NILSSON,M.HAMALAINEN,M.IVARSSON,J.GOTTFRIES, JRNL AUTH 2 Y.XUE,S.HANSSON,R.ISAKSSON,T.FEX JRNL TITL COMPOUNDS BINDING TO THE S2-S3 POCKETS OF THROMBIN. JRNL REF J.MED.CHEM. V. 52 2708 2009 JRNL REFN ISSN 0022-2623 JRNL PMID 19371038 JRNL DOI 10.1021/JM8011849

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 29462 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1570 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1993 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2540 REMARK 3 BIN FREE R VALUE SET COUNT : 109 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2332 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 29 REMARK 3 SOLVENT ATOMS : 277 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.77000 REMARK 3 B22 (A**2) : -1.05000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.126 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2422 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3270 ; 1.301 ; 1.977 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 5.859 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 115 ;30.694 ;23.391 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 426 ;12.888 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;12.096 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 335 ; 0.089 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1840 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1122 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1631 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 233 ; 0.119 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.046 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 24 ; 0.429 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 17 ; 0.178 ; 0.200 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): 1424 ; 0.795 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2295 ; 1.484 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1050 ; 2.138 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 975 ; 3.467 ; 4.500 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 : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 REMARK 3 RIDING POSITIONS

REMARK 4 REMARK 4 3DA9 COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-AUG-08. REMARK 100 THE RCSB ID CODE IS RCSB047788.

REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 70.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : 0.06500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.57000 REMARK 200 R SYM FOR SHELL (I) : 0.53000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CCP4 REMARK 200 STARTING MODEL: APO REMARK 200 REMARK 200 REMARK: NULL

REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE DROP WAS MADE BY MIXING 1.5 UL REMARK 280 OF THE THROMBIN-HIRUDIN COMPLEX AND 1.5 UL OF RESERVIOR REMARK 280 SOLUTION CONTAINING: PHOSPHATE BUFFER PH7.3, 28% PEG, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K

REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 34.91500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.72750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 34.91500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 35.72750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D 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 THR A 1 REMARK 465 PHE A 2 REMARK 465 GLY A 3 REMARK 465 SER A 4 REMARK 465 GLY A 5 REMARK 465 GLU A 6 REMARK 465 ASP A 34 REMARK 465 GLY A 35 REMARK 465 ARG A 36 REMARK 465 TRP B 183A REMARK 465 THR B 183B REMARK 465 ALA B 183C REMARK 465 ASN B 183D REMARK 465 VAL B 183E REMARK 465 GLY B 183F REMARK 465 LYS B 183G REMARK 465 GLU B 289

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 CD ARG B 106 CD ARG B 106 2555 2.17 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 PHE A 15 -87.71 -130.20 REMARK 500 TYR B 83 83.55 -154.47 REMARK 500 ASN B 89 76.87 -157.85 REMARK 500 HIS B 102 -60.98 -131.89 REMARK 500 ILE B 111 -59.76 -126.30 REMARK 500 REMARK 500 REMARK: NULL

REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 614 DISTANCE = 5.47 ANGSTROMS

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 NA B 402 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG B 263 O REMARK 620 2 LYS B 266 O 93.2 REMARK 620 3 HOH B 628 O 100.0 82.5 REMARK 620 4 HOH B 629 O 107.9 158.4 98.1 REMARK 620 5 HOH B 414 O 159.7 69.8 89.0 88.6 REMARK 620 6 HOH B 429 O 87.6 90.1 169.7 86.1 81.6 REMARK 620 N 1 2 3 4 5

REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 402 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 44U B 1

DBREF 3DA9 A 1 36 UNP P00734 THRB_HUMAN 328 363 DBREF 3DA9 B 37 289 UNP P00734 THRB_HUMAN 364 622 DBREF 3DA9 D 355 363 PDB 3DA9 3DA9 355 363

SEQRES 1 A 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 A 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 A 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 B 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 B 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 B 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 B 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 B 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 B 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 B 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 B 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 B 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 B 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 B 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 B 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 B 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 B 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 B 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 B 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 B 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 B 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 B 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 B 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 D 9 ASP PHE GLU GLU ILE PRO GLY GLU PTR

MODRES 3DA9 PTR D 363 TYR O-PHOSPHOTYROSINE

HET PTR D 363 16 HET NA B 402 1 HET 44U B 1 28

HETNAM PTR O-PHOSPHOTYROSINE HETNAM NA SODIUM ION HETNAM 44U BETA-PHENYL-D-PHENYLALANYL-N-PROPYL-L-PROLINAMIDE

HETSYN PTR PHOSPHONOTYROSINE

FORMUL 3 PTR C9 H12 N O6 P FORMUL 4 NA NA 1+ FORMUL 5 44U C23 H29 N3 O2 FORMUL 6 HOH *277(H2 O)

HELIX 1 1 PHE A 15 SER A 19 5 5 HELIX 2 2 THR A 24 TYR A 32 1 9 HELIX 3 3 ALA B 77 CYS B 80 5 4 HELIX 4 4 PRO B 84 ASP B 87 5 4 HELIX 5 5 THR B 91 ASN B 93 5 3 HELIX 6 6 ASP B 158 LEU B 166 1 9 HELIX 7 7 GLU B 199 SER B 206 1 8 HELIX 8 8 LYS B 221 GLY B 225 5 5 HELIX 9 9 LEU B 276 GLY B 288 1 13

SHEET 1 A 7 SER B 41 ASP B 42 0 SHEET 2 A 7 GLN B 191 PRO B 196 -1 O VAL B 192 N SER B 41 SHEET 3 A 7 LYS B 171 GLY B 176 -1 N VAL B 174 O VAL B 193 SHEET 4 A 7 PRO B 238 LYS B 242 -1 O VAL B 240 N ARG B 173 SHEET 5 A 7 TRP B 249 TRP B 257 -1 O TYR B 250 N MET B 241 SHEET 6 A 7 GLY B 268 HIS B 272 -1 O PHE B 269 N TRP B 257 SHEET 7 A 7 MET B 215 ALA B 218 -1 N PHE B 216 O TYR B 270 SHEET 1 B 7 GLN B 51 ARG B 56 0 SHEET 2 B 7 GLU B 61 LEU B 68 -1 O LEU B 63 N LEU B 54 SHEET 3 B 7 TRP B 73 THR B 76 -1 O LEU B 75 N SER B 67 SHEET 4 B 7 ALA B 137 LEU B 141 -1 O ALA B 137 N THR B 76 SHEET 5 B 7 LYS B 113 ILE B 122 -1 N TYR B 121 O LEU B 138 SHEET 6 B 7 LEU B 95 ILE B 99 -1 N VAL B 97 O SER B 115 SHEET 7 B 7 GLN B 51 ARG B 56 -1 N PHE B 55 O LEU B 96 SHEET 1 C 2 LEU B 82 TYR B 83 0 SHEET 2 C 2 LYS B 88 ASN B 89 -1 O LYS B 88 N TYR B 83

SSBOND 1 CYS A 9 CYS B 155 1555 1555 2.06 SSBOND 2 CYS B 64 CYS B 80 1555 1555 2.03 SSBOND 3 CYS B 203 CYS B 217 1555 1555 2.03 SSBOND 4 CYS B 231 CYS B 261 1555 1555 2.04

LINK C GLU D 362 N PTR D 363 1555 1555 1.33 LINK O ARG B 263 NA NA B 402 1555 1555 2.39 LINK O LYS B 266 NA NA B 402 1555 1555 2.40 LINK NA NA B 402 O HOH B 628 1555 1555 2.32 LINK NA NA B 402 O HOH B 629 1555 1555 2.39 LINK NA NA B 402 O HOH B 414 1555 1555 2.52 LINK NA NA B 402 O HOH B 429 1555 1555 2.64

CISPEP 1 SER B 58 PRO B 59 0 -6.42

SITE 1 AC1 6 ARG B 263 LYS B 266 HOH B 414 HOH B 429 SITE 2 AC1 6 HOH B 628 HOH B 629 SITE 1 AC2 14 HIS B 79 TYR B 83 GLU B 130 ASN B 131 SITE 2 AC2 14 ILE B 209 CYS B 231 SER B 235 SER B 256 SITE 3 AC2 14 TRP B 257 GLY B 258 GLU B 259 HOH B 532 SITE 4 AC2 14 HOH B 547 HOH B 572

CRYST1 69.830 71.455 71.905 90.00 100.35 90.00 C 1 2 1 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 0.014320 0.000000 0.002615 0.00000

SCALE2 0.000000 0.013995 0.000000 0.00000

SCALE3 0.000000 0.000000 0.014137 0.00000