10 20 30 40 50 60 70 80 5EW2 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER PROTEIN/DNA 20-NOV-15 5EW2
TITLE HUMAN THROMBIN SANDWICHED BETWEEN TWO DNA APTAMERS: HD22 AND HD1- TITLE 2 DELTAT12
COMPND MOL_ID: 1; COMPND 2 MOLECULE: THROMBIN LIGHT CHAIN; COMPND 3 CHAIN: L; COMPND 4 SYNONYM: COAGULATION FACTOR II; COMPND 5 EC: 3.4.21.5; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: THROMBIN HEAVY CHAIN; COMPND 8 CHAIN: H; COMPND 9 SYNONYM: COAGULATION FACTOR II; COMPND 10 EC: 3.4.21.5; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HD22 (27MER); COMPND 13 CHAIN: D; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 4; COMPND 16 MOLECULE: HD1-DELTAT12; COMPND 17 CHAIN: E; COMPND 18 ENGINEERED: YES; COMPND 19 OTHER_DETAILS: HD1 VARIANT IN WHICH NUCLEOBASE OF T12 HAS BEEN COMPND 20 DELETED
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; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 4; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606
KEYWDS PROTEIN-DNA COMPLEX, BLOOD COAGULATION, DNA APTAMER, DNA-INHIBITOR, KEYWDS 2 G-QUADRUPLEX, DUPLEX-QUADRUPLEX JUNCTION, SERINE PROTEASE, KEYWDS 3 HYDROLASE, ABASIC FURAN, HYDROLASE-DNA COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR A.PICA,I.RUSSO KRAUSS,V.PARENTE,F.SICA
REVDAT 4 18-JAN-17 5EW2 1 JRNL REVDAT 3 21-DEC-16 5EW2 1 REMARK REVDAT 2 14-DEC-16 5EW2 1 JRNL REVDAT 1 30-NOV-16 5EW2 0
JRNL AUTH A.PICA,I.RUSSO KRAUSS,V.PARENTE,H.TATEISHI-KARIMATA, JRNL AUTH 2 S.NAGATOISHI,K.TSUMOTO,N.SUGIMOTO,F.SICA JRNL TITL THROUGH-BOND EFFECTS IN THE TERNARY COMPLEXES OF THROMBIN JRNL TITL 2 SANDWICHED BY TWO DNA APTAMERS. JRNL REF NUCLEIC ACIDS RES. V. 45 461 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 27899589 JRNL DOI 10.1093/NAR/GKW1113
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.RUSSO KRAUSS,A.PICA,A.MERLINO,L.MAZZARELLA,F.SICA REMARK 1 TITL DUPLEX-QUADRUPLEX MOTIFS IN A PECULIAR STRUCTURAL REMARK 1 TITL 2 ORGANIZATION COOPERATIVELY CONTRIBUTE TO THROMBIN BINDING OF REMARK 1 TITL 3 A DNA APTAMER. REMARK 1 REF ACTA CRYSTALLOGR. D BIOL. V. 69 2403 2013 REMARK 1 REF 2 CRYSTALLOGR. REMARK 1 REFN ESSN 1399-0047 REMARK 1 PMID 24311581 REMARK 1 DOI 10.1107/S0907444913022269 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.PICA,I.RUSSO KRAUSS,A.MERLINO,S.NAGATOISHI,N.SUGIMOTO, REMARK 1 AUTH 2 F.SICA REMARK 1 TITL DISSECTING THE CONTRIBUTION OF THROMBIN EXOSITE I IN THE REMARK 1 TITL 2 RECOGNITION OF THROMBIN BINDING APTAMER. REMARK 1 REF FEBS J. V. 280 6581 2013 REMARK 1 REFN ISSN 1742-4658 REMARK 1 PMID 24128303 REMARK 1 DOI 10.1111/FEBS.12561
REMARK 2 REMARK 2 RESOLUTION. 3.59 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 3.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 90.8 REMARK 3 NUMBER OF REFLECTIONS : 5167 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 271 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) : 3.59 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 219 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.89 REMARK 3 BIN R VALUE (WORKING SET) : 0.2850 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2260 REMARK 3 NUCLEIC ACID ATOMS : 832 REMARK 3 HETEROGEN ATOMS : 47 REMARK 3 SOLVENT ATOMS : 7 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 70.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.99000 REMARK 3 B22 (A**2) : 1.49000 REMARK 3 B33 (A**2) : -0.26000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.47000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.570 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 : 0.895 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.859 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3299 ; 0.015 ; 0.017 REMARK 3 BOND LENGTHS OTHERS (A): 2695 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4640 ; 1.855 ; 1.724 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6247 ; 1.237 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 276 ; 6.534 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;33.375 ;23.273 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 417 ;16.483 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;10.740 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 452 ; 0.118 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3096 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 737 ; 0.003 ; 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): 1116 ; 1.569 ; 3.836 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1117 ; 1.568 ; 3.836 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1388 ; 2.734 ; 5.752 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1389 ; 2.733 ; 5.751 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2183 ; 2.073 ; 4.332 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2182 ; 2.074 ; 4.332 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3253 ; 3.603 ; 6.478 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 14184 ; 7.595 ;39.907 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 14183 ; 7.590 ;39.908 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : L 1 L 14 REMARK 3 ORIGIN FOR THE GROUP (A): -12.5517 29.6449 26.5447 REMARK 3 T TENSOR REMARK 3 T11: 0.1401 T22: 0.2637 REMARK 3 T33: 1.0309 T12: -0.1408 REMARK 3 T13: -0.0519 T23: -0.2887 REMARK 3 L TENSOR REMARK 3 L11: 5.9265 L22: 2.2683 REMARK 3 L33: 3.8518 L12: 1.2961 REMARK 3 L13: -0.6886 L23: -1.1844 REMARK 3 S TENSOR REMARK 3 S11: -0.2949 S12: -0.2269 S13: 1.6795 REMARK 3 S21: -0.1198 S22: 0.3894 S23: -0.6251 REMARK 3 S31: -0.1524 S32: 0.0437 S33: -0.0945 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 16 H 246 REMARK 3 ORIGIN FOR THE GROUP (A): -25.1854 15.5941 23.9870 REMARK 3 T TENSOR REMARK 3 T11: 0.0549 T22: 0.0950 REMARK 3 T33: 0.0489 T12: -0.0189 REMARK 3 T13: 0.0111 T23: -0.0262 REMARK 3 L TENSOR REMARK 3 L11: 5.7149 L22: 3.3266 REMARK 3 L33: 2.5072 L12: 0.0246 REMARK 3 L13: 0.5818 L23: 0.3858 REMARK 3 S TENSOR REMARK 3 S11: -0.2540 S12: 0.0162 S13: 0.1101 REMARK 3 S21: 0.1565 S22: 0.4006 S23: 0.0425 REMARK 3 S31: 0.0191 S32: 0.0472 S33: -0.1466 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 2 D 26 REMARK 3 ORIGIN FOR THE GROUP (A): -48.2681 19.7699 16.2639 REMARK 3 T TENSOR REMARK 3 T11: 0.1083 T22: 0.2909 REMARK 3 T33: 0.6444 T12: -0.1085 REMARK 3 T13: -0.0900 T23: 0.1598 REMARK 3 L TENSOR REMARK 3 L11: 4.7521 L22: 2.6528 REMARK 3 L33: 5.7599 L12: -0.5379 REMARK 3 L13: 0.1815 L23: -1.1933 REMARK 3 S TENSOR REMARK 3 S11: -0.4809 S12: 0.3790 S13: 0.6995 REMARK 3 S21: -0.1250 S22: 0.4201 S23: 0.6893 REMARK 3 S31: -0.1411 S32: -0.7463 S33: 0.0607 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : E 1 E 15 REMARK 3 ORIGIN FOR THE GROUP (A): -4.0337 6.1274 44.8645 REMARK 3 T TENSOR REMARK 3 T11: 0.6983 T22: 0.9732 REMARK 3 T33: 0.2971 T12: 0.3153 REMARK 3 T13: -0.2201 T23: -0.0430 REMARK 3 L TENSOR REMARK 3 L11: 4.6085 L22: 3.9519 REMARK 3 L33: 0.6521 L12: 2.7805 REMARK 3 L13: 0.4233 L23: -0.5020 REMARK 3 S TENSOR REMARK 3 S11: 0.3555 S12: -0.9524 S13: -0.8502 REMARK 3 S21: 0.5931 S22: -0.2629 S23: -0.8318 REMARK 3 S31: 0.2829 S32: 0.2820 S33: -0.0926 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS
REMARK 4 REMARK 4 5EW2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-NOV-15. REMARK 100 THE DEPOSITION ID IS D_1000215521.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-NOV-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5755 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.580 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 2.800 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.46600 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: PHASER 2.5.7, PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 3350, 0.2 M SODIUM FORMATE, 2% REMARK 280 ACETONITRILE, VAPOR 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 58.54450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.64800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.54450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.64800 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, D, E 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 L -4 REMARK 465 PHE L -3 REMARK 465 GLY L -2 REMARK 465 SER L -1 REMARK 465 GLY L 0 REMARK 465 ASP L 15 REMARK 465 GLY L 16 REMARK 465 ARG L 17 REMARK 465 TRP H 147A REMARK 465 THR H 147B REMARK 465 ALA H 147C REMARK 465 ASN H 147D REMARK 465 VAL H 147E REMARK 465 GLY H 147F REMARK 465 LYS H 147G REMARK 465 GLU H 247 REMARK 465 DG D 1 REMARK 465 DC D 27
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 O LEU L 14F OG SER L 14I 2.00 REMARK 500 ND2 ASN H 60G C1 NAG H 301 2.12 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 ARG H 187 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 DG D 25 O5' - P - OP1 ANGL. DEV. = -6.0 DEGREES REMARK 500 DT E 7 C1' - O4' - C4' ANGL. DEV. = -7.5 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 PHE L 7 -72.60 -128.37 REMARK 500 GLN H 38 93.45 -68.28 REMARK 500 ASN H 60G 88.97 -157.09 REMARK 500 HIS H 71 -56.35 -132.98 REMARK 500 ASN H 78 17.75 57.19 REMARK 500 ILE H 79 -52.92 -124.40 REMARK 500 ASN H 98 18.62 -163.65 REMARK 500 SER H 115 -167.97 -168.81 REMARK 500 ASN H 204B 10.58 -144.98 REMARK 500 SER H 214 -64.06 -107.83 REMARK 500 REMARK 500 REMARK: NULL
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 NAG H 301
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 D 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG D 8 O6 REMARK 620 2 DG D 11 O6 83.8 REMARK 620 3 DG D 17 O6 172.8 95.3 REMARK 620 4 DG D 20 O6 85.9 169.7 95.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA E 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG E 1 O6 REMARK 620 2 DG E 2 O6 65.6 REMARK 620 3 DG E 5 O6 118.1 71.4 REMARK 620 4 DG E 6 O6 73.3 104.0 76.5 REMARK 620 5 DG E 10 O6 122.8 168.6 97.2 73.3 REMARK 620 6 DG E 11 O6 167.3 109.8 69.1 119.4 63.8 REMARK 620 7 DG E 14 O6 101.7 65.2 98.2 169.1 117.1 66.1 REMARK 620 8 DG E 15 O6 73.9 111.1 166.5 114.6 79.7 98.0 72.2 REMARK 620 N 1 2 3 4 5 6 7
REMARK 630 REMARK 630 MOLECULE TYPE: PEPTIDE-LIKE INHIBITOR REMARK 630 MOLECULE NAME: D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO)METHYL] REMARK 630 AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L-PROLINAMIDE REMARK 630 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 630 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 630 REMARK 630 M RES C SSSEQI REMARK 630 0G6 H 302 REMARK 630 SOURCE: NULL REMARK 630 TAXONOMY: NULL REMARK 630 SUBCOMP: DPN PRO AR7 0QE REMARK 630 DETAILS: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAG H 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0G6 H 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA H 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA D 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA E 101
DBREF 5EW2 L -4 17 UNP P00734 THRB_HUMAN 328 363 DBREF 5EW2 H 16 247 UNP P00734 THRB_HUMAN 364 622 DBREF 5EW2 D 1 27 PDB 5EW2 5EW2 1 27 DBREF 5EW2 E 1 15 PDB 5EW2 5EW2 1 15
SEQRES 1 L 36 THR PHE GLY SER GLY GLU ALA ASP CYS GLY LEU ARG PRO SEQRES 2 L 36 LEU PHE GLU LYS LYS SER LEU GLU ASP LYS THR GLU ARG SEQRES 3 L 36 GLU LEU LEU GLU SER TYR ILE ASP GLY ARG SEQRES 1 H 259 ILE VAL GLU GLY SER ASP ALA GLU ILE GLY MET SER PRO SEQRES 2 H 259 TRP GLN VAL MET LEU PHE ARG LYS SER PRO GLN GLU LEU SEQRES 3 H 259 LEU CYS GLY ALA SER LEU ILE SER ASP ARG TRP VAL LEU SEQRES 4 H 259 THR ALA ALA HIS CYS LEU LEU TYR PRO PRO TRP ASP LYS SEQRES 5 H 259 ASN PHE THR GLU ASN ASP LEU LEU VAL ARG ILE GLY LYS SEQRES 6 H 259 HIS SER ARG THR ARG TYR GLU ARG ASN ILE GLU LYS ILE SEQRES 7 H 259 SER MET LEU GLU LYS ILE TYR ILE HIS PRO ARG TYR ASN SEQRES 8 H 259 TRP ARG GLU ASN LEU ASP ARG ASP ILE ALA LEU MET LYS SEQRES 9 H 259 LEU LYS LYS PRO VAL ALA PHE SER ASP TYR ILE HIS PRO SEQRES 10 H 259 VAL CYS LEU PRO ASP ARG GLU THR ALA ALA SER LEU LEU SEQRES 11 H 259 GLN ALA GLY TYR LYS GLY ARG VAL THR GLY TRP GLY ASN SEQRES 12 H 259 LEU LYS GLU THR TRP THR ALA ASN VAL GLY LYS GLY GLN SEQRES 13 H 259 PRO SER VAL LEU GLN VAL VAL ASN LEU PRO ILE VAL GLU SEQRES 14 H 259 ARG PRO VAL CYS LYS ASP SER THR ARG ILE ARG ILE THR SEQRES 15 H 259 ASP ASN MET PHE CYS ALA GLY TYR LYS PRO ASP GLU GLY SEQRES 16 H 259 LYS ARG GLY ASP ALA CYS GLU GLY ASP SER GLY GLY PRO SEQRES 17 H 259 PHE VAL MET LYS SER PRO PHE ASN ASN ARG TRP TYR GLN SEQRES 18 H 259 MET GLY ILE VAL SER TRP GLY GLU GLY CYS ASP ARG ASP SEQRES 19 H 259 GLY LYS TYR GLY PHE TYR THR HIS VAL PHE ARG LEU LYS SEQRES 20 H 259 LYS TRP ILE GLN LYS VAL ILE ASP GLN PHE GLY GLU SEQRES 1 D 27 DG DT DC DC DG DT DG DG DT DA DG DG DG SEQRES 2 D 27 DC DA DG DG DT DT DG DG DG DG DT DG DA SEQRES 3 D 27 DC SEQRES 1 E 15 DG DG DT DT DG DG DT DG DT DG DG 3DR DT SEQRES 2 E 15 DG DG
HET 3DR E 12 11 HET NAG H 301 14 HET 0G6 H 302 30 HET NA H 303 1 HET NA D 101 1 HET NA E 101 1
HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM NAG N-ACETYL-D-GLUCOSAMINE HETNAM 0G6 D-PHENYLALANYL-N-[(2S,3S)-6-{[AMINO(IMINIO) HETNAM 2 0G6 METHYL]AMINO}-1-CHLORO-2-HYDROXYHEXAN-3-YL]-L- HETNAM 3 0G6 PROLINAMIDE HETNAM NA SODIUM ION
HETSYN 3DR ABASIC DIDEOXYRIBOSE HETSYN 0G6 PPACK
FORMUL 4 3DR C5 H11 O6 P FORMUL 5 NAG C8 H15 N O6 FORMUL 6 0G6 C21 H34 CL N6 O3 1+ FORMUL 7 NA 3(NA 1+) FORMUL 10 HOH *7(H2 O)
HELIX 1 AA1 PHE L 7 SER L 11 5 5 HELIX 2 AA2 THR L 14B TYR L 14J 1 9 HELIX 3 AA3 ALA H 55 CYS H 58 5 4 HELIX 4 AA4 PRO H 60B ASP H 60E 5 4 HELIX 5 AA5 THR H 60I ASN H 62 5 3 HELIX 6 AA6 ASP H 125 LEU H 130 1 9 HELIX 7 AA7 GLU H 164 SER H 171 1 8 HELIX 8 AA8 LYS H 185 GLY H 186C 5 5 HELIX 9 AA9 LEU H 234 GLY H 246 1 13
SHEET 1 AA1 7 SER H 20 ASP H 21 0 SHEET 2 AA1 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20 SHEET 3 AA1 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158 SHEET 4 AA1 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137 SHEET 5 AA1 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201 SHEET 6 AA1 7 GLY H 226 HIS H 230 -1 O THR H 229 N ILE H 212 SHEET 7 AA1 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228 SHEET 1 AA2 7 GLN H 30 ARG H 35 0 SHEET 2 AA2 7 GLU H 39 LEU H 46 -1 O CYS H 42 N LEU H 33 SHEET 3 AA2 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45 SHEET 4 AA2 7 ALA H 104 LEU H 108 -1 O ALA H 104 N THR H 54 SHEET 5 AA2 7 LYS H 81 ILE H 90 -1 N GLU H 86 O LYS H 107 SHEET 6 AA2 7 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81 SHEET 7 AA2 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65 SHEET 1 AA3 2 LEU H 60 TYR H 60A 0 SHEET 2 AA3 2 LYS H 60F ASN H 60G-1 O LYS H 60F N TYR H 60A
SSBOND 1 CYS L 1 CYS H 122 1555 1555 2.00 SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.03 SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03 SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.04
LINK NE2 HIS H 57 C3 0G6 H 302 1555 1555 1.48 LINK OG SER H 195 C2 0G6 H 302 1555 1555 1.43 LINK O LYS H 224 NA NA H 303 1555 1555 2.64 LINK O6 DG D 8 NA NA D 101 1555 1555 2.29 LINK O6 DG D 11 NA NA D 101 1555 1555 2.03 LINK O6 DG D 17 NA NA D 101 1555 1555 2.06 LINK O6 DG D 20 NA NA D 101 1555 1555 2.05 LINK O6 DG E 1 NA NA E 101 1555 1555 2.43 LINK O6 DG E 2 NA NA E 101 1555 1555 2.93 LINK O6 DG E 5 NA NA E 101 1555 1555 2.51 LINK O6 DG E 6 NA NA E 101 1555 1555 2.65 LINK O6 DG E 10 NA NA E 101 1555 1555 2.47 LINK O3' DG E 11 P 3DR E 12 1555 1555 1.57 LINK O6 DG E 11 NA NA E 101 1555 1555 2.86 LINK O3' 3DR E 12 P DT E 13 1555 1555 1.62 LINK O6 DG E 14 NA NA E 101 1555 1555 2.59 LINK O6 DG E 15 NA NA E 101 1555 1555 2.89
CISPEP 1 SER H 36A PRO H 37 0 -3.56
SITE 1 AC1 1 ASN H 60G SITE 1 AC2 12 HIS H 57 LEU H 99 ILE H 174 ASP H 189 SITE 2 AC2 12 ALA H 190 GLY H 193 SER H 195 SER H 214 SITE 3 AC2 12 TRP H 215 GLY H 216 GLY H 219 GLY H 226 SITE 1 AC3 2 ARG H 221 LYS H 224 SITE 1 AC4 8 DG D 5 DG D 7 DG D 8 DG D 11 SITE 2 AC4 8 DG D 12 DG D 16 DG D 17 DG D 20 SITE 1 AC5 8 DG E 1 DG E 2 DG E 5 DG E 6 SITE 2 AC5 8 DG E 10 DG E 11 DG E 14 DG E 15
CRYST1 117.089 41.296 104.923 90.00 102.90 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 0.008541 0.000000 0.001956 0.00000
SCALE2 0.000000 0.024215 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009777 0.00000