HEADER HYDROLASE/HYDROLASE INHIBITOR/DNA 31-JAN-12 4DIH
TITLE X-RAY STRUCTURE OF THE COMPLEX BETWEEN HUMAN ALPHA THROMBIN AND
TITLE 2 THROMBIN BINDING APTAMER IN THE PRESENCE OF SODIUM IONS
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTHROMBIN;
COMPND 3 CHAIN: L;
COMPND 4 FRAGMENT: LIGHT CHAIN FRAGMENT (UNP RESIDUES 328-363);
COMPND 5 SYNONYM: COAGULATION FACTOR II, THROMBIN LIGHT CHAIN;
COMPND 6 MOL_ID: 2;
COMPND 7 MOLECULE: PROTHROMBIN;
COMPND 8 CHAIN: H;
COMPND 9 FRAGMENT: HEAVY CHAIN FRAGMENT (UNP RESIDUES 364-622);
COMPND 10 SYNONYM: COAGULATION FACTOR II, THROMBIN HEAVY CHAIN;
COMPND 11 EC: 3.4.21.5;
COMPND 12 MOL_ID: 3;
COMPND 13 MOLECULE: THROMBIN BINDING APTAMER;
COMPND 14 CHAIN: D;
COMPND 15 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;
SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC DNA;
SOURCE 12 ORGANISM_TAXID: 32630
KEYWDS PROTEIN-DNA COMPLEX, SERINE PROTEASE, BLOOD COAGULATION, APTAMER,
KEYWDS 2 HYDROLASE-HYDROLASE INHIBITOR-DNA COMPLEX, SERINE PROTEASE FOLD, DNA
KEYWDS 3 APTAMER, BLOOD, G-QUADRUPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR I.RUSSO KRAUSS,A.MERLINO,L.MAZZARELLA,F.SICA
REVDAT 4 13-SEP-23 4DIH 1 HETSYN
REVDAT 3 29-JUL-20 4DIH 1 COMPND REMARK HETNAM LINK
REVDAT 3 2 1 SITE
REVDAT 2 26-SEP-12 4DIH 1 JRNL
REVDAT 1 18-JUL-12 4DIH 0
JRNL AUTH I.RUSSO KRAUSS,A.MERLINO,A.RANDAZZO,E.NOVELLINO,
JRNL AUTH 2 L.MAZZARELLA,F.SICA
JRNL TITL HIGH-RESOLUTION STRUCTURES OF TWO COMPLEXES BETWEEN THROMBIN
JRNL TITL 2 AND THROMBIN-BINDING APTAMER SHED LIGHT ON THE ROLE OF
JRNL TITL 3 CATIONS IN THE APTAMER INHIBITORY ACTIVITY.
JRNL REF NUCLEIC ACIDS RES. V. 40 8119 2012
JRNL REFN ISSN 0305-1048
JRNL PMID 22669903
JRNL DOI 10.1093/NAR/GKS512
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH I.RUSSO KRAUSS,A.MERLINO,C.GIANCOLA,A.RANDAZZO,L.MAZZARELLA,
REMARK 1 AUTH 2 F.SICA
REMARK 1 TITL THROMBIN-APTAMER RECOGNITION: A REVEALED AMBIGUITY.
REMARK 1 REF NUCLEIC ACIDS RES. V. 39 7858 2011
REMARK 1 REFN ISSN 0305-1048
REMARK 1 PMID 21715374
REMARK 1 DOI 10.1093/NAR/GKR522
REMARK 1 REFERENCE 2
REMARK 1 AUTH K.PADMANABHAN,K.P.PADMANABHAN,J.D.FERRARA,J.E.SADLER,
REMARK 1 AUTH 2 A.TULINSKY
REMARK 1 TITL THE STRUCTURE OF ALPHA-THROMBIN INHIBITED BY A 15-MER
REMARK 1 TITL 2 SINGLE-STRANDED DNA APTAMER.
REMARK 1 REF J.BIOL.CHEM. V. 268 17651 1993
REMARK 1 REFN ISSN 0021-9258
REMARK 1 PMID 8102368
REMARK 1 REFERENCE 3
REMARK 1 AUTH K.PADMANABHAN,A.TULINSKY
REMARK 1 TITL AN AMBIGUOUS STRUCTURE OF A DNA 15-MER THROMBIN COMPLEX.
REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 52 272 1996
REMARK 1 REFN ISSN 0907-4449
REMARK 1 PMID 15299700
REMARK 1 DOI 10.1107/S0907444995013977
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 26555
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3 R VALUE (WORKING SET) : 0.167
REMARK 3 FREE R VALUE : 0.213
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : 1282
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL
REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2243
REMARK 3 NUCLEIC ACID ATOMS : 306
REMARK 3 HETEROGEN ATOMS : 51
REMARK 3 SOLVENT ATOMS : 217
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) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : 1.549 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.197 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.151 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.169 ; 2.500
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4DIH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-FEB-12.
REMARK 100 THE DEPOSITION ID IS D_1000070370.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 11-MAR-10
REMARK 200 TEMPERATURE (KELVIN) : 100.0
REMARK 200 PH : 7.4
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
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : MIRRORS
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 : 28160
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 90.9
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
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) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 75.6
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
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: CNS
REMARK 200 STARTING MODEL: PDB ENTRY 3QLP AND 1HAO
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.91
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 10-15% W/V POLYETHYLENE GLYCOL 8000,
REMARK 280 0.05 M ZINC ACETATE, 0.1 M SODIUM CACODYLATE , PH 7.4, VAPOR
REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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 300 REMARK: 1:1 PROTEIN-DNA APTAMER COMPLEX
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: 4310 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 14160 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -113.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, 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 L -5
REMARK 465 PHE L -4
REMARK 465 GLY L -3
REMARK 465 SER L -2
REMARK 465 GLY L -1
REMARK 465 GLU 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 GLY H 147H
REMARK 465 GLY H 246
REMARK 465 GLU H 247
REMARK 470
REMARK 470 MISSING ATOM
REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER;
REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER;
REMARK 470 I=INSERTION CODE):
REMARK 470 M RES CSSEQI ATOMS
REMARK 470 DT D 9 N1 C2 O2 N3 C4 O4 C5
REMARK 470 DT D 9 C7 C6
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 OE1 GLN H 30 O HOH H 475 2.14
REMARK 500 O HOH H 414 O HOH H 517 2.14
REMARK 500 C PHE H 245 O HOH H 518 2.19
REMARK 500 NH2 ARG H 35 O HOH H 547 2.19
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 L 4 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES
REMARK 500 ARG H 93 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES
REMARK 500 ARG H 93 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES
REMARK 500 TYR H 117 CB - CG - CD1 ANGL. DEV. = -3.9 DEGREES
REMARK 500 ARG H 233 NE - CZ - NH1 ANGL. DEV. = 4.3 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 -84.97 -127.81
REMARK 500 TYR H 60A 87.49 -155.07
REMARK 500 ASN H 60G 79.93 -155.33
REMARK 500 HIS H 71 -57.92 -130.67
REMARK 500 ASN H 98 13.57 -142.48
REMARK 500
REMARK 500 REMARK: NULL
REMARK 600
REMARK 600 HETEROGEN
REMARK 600
REMARK 600 THE INHIBITOR IS COVALENTLY CONNECTED TO ACTIVE_SITE RESIDUES:
REMARK 600
REMARK 600 1) VIA A HEMIKETAL GROUP TO OG SER 195 IN CHAIN H
REMARK 600 2) VIA A METHYLENE GROUP TO NE2 HIS 57 IN CHAIN H
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 ZN L 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ASP L 1A OD1
REMARK 620 2 HOH L 203 O 122.4
REMARK 620 3 HIS H 119 NE2 113.2 109.0
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN H 305 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU H 86 OE2
REMARK 620 2 HOH H 402 O 98.4
REMARK 620 3 HOH H 403 O 124.4 123.7
REMARK 620 4 HOH H 523 O 113.4 104.0 91.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 NA H 303 NA
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 ARG H 221 O
REMARK 620 2 LYS H 224 O 90.8
REMARK 620 3 HOH H 428 O 88.8 86.5
REMARK 620 4 HOH H 429 O 93.8 81.3 167.5
REMARK 620 5 HOH H 437 O 151.6 64.5 76.6 95.8
REMARK 620 6 HOH H 456 O 108.8 159.5 87.9 102.8 95.0
REMARK 620 N 1 2 3 4 5
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 1 O6
REMARK 620 2 DG D 2 O6 64.3
REMARK 620 3 DG D 6 O6 70.0 91.6
REMARK 620 4 DG D 10 O6 118.5 150.8 65.3
REMARK 620 5 DG D 11 O6 169.4 105.7 108.3 68.3
REMARK 620 6 DG D 14 O6 102.5 66.2 157.3 133.4 74.9
REMARK 620 7 DG D 15 O6 82.0 127.2 114.5 80.5 107.7 84.5
REMARK 620 N 1 2 3 4 5 6
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 1 O6
REMARK 620 2 DG D 2 O6 66.8
REMARK 620 3 DG D 5 O6 124.5 75.4
REMARK 620 4 DG D 6 O6 73.8 108.1 81.6
REMARK 620 5 DG D 10 O6 107.2 174.0 109.0 69.1
REMARK 620 6 DG D 11 O6 152.4 118.0 81.4 124.2 67.3
REMARK 620 7 DG D 14 O6 89.2 66.6 111.5 162.6 114.5 70.6
REMARK 620 8 DG D 15 O6 65.0 110.4 170.5 103.1 65.9 89.2 65.7
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 301
REMARK 630 SOURCE: NULL
REMARK 630 TAXONOMY: NULL
REMARK 630 SUBCOMP: DPN PRO AR7 0QE
REMARK 630 DETAILS: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 4DII RELATED DB: PDB
REMARK 900 THE SAME COMPLEX IN THE PRESENCE OF K+ ION
DBREF 4DIH L -5 17 UNP P00734 THRB_HUMAN 328 363
DBREF 4DIH H 16 247 UNP P00734 THRB_HUMAN 364 622
DBREF 4DIH D 1 15 PDB 4DIH 4DIH 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 15 DG DG DT DT DG DG DT DG DT DG DG DT DT
SEQRES 2 D 15 DG DG
MODRES 4DIH ASN H 60G ASN GLYCOSYLATION SITE
HET ZN L 101 1
HET 0G6 H 301 30
HET NAG H 302 14
HET NA H 303 1
HET ZN H 304 1
HET ZN H 305 1
HET CL H 306 1
HET CL H 307 1
HET NA D 101 2
HETNAM ZN ZINC ION
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 NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
HETNAM NA SODIUM ION
HETNAM CL CHLORIDE ION
HETSYN 0G6 PPACK
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
FORMUL 4 ZN 3(ZN 2+)
FORMUL 5 0G6 C21 H34 CL N6 O3 1+
FORMUL 6 NAG C8 H15 N O6
FORMUL 7 NA 2(NA 1+)
FORMUL 10 CL 2(CL 1-)
FORMUL 13 HOH *217(H2 O)
HELIX 1 1 PHE L 7 SER L 11 5 5
HELIX 2 2 THR L 14B ILE L 14K 1 10
HELIX 3 3 ALA H 55 CYS H 58 5 4
HELIX 4 4 PRO H 60B ASP H 60E 5 4
HELIX 5 5 THR H 60I ASN H 62 5 3
HELIX 6 6 ASP H 125 LEU H 130 1 9
HELIX 7 7 GLU H 164 SER H 171 1 8
HELIX 8 8 LEU H 234 PHE H 245 1 12
SHEET 1 A 7 SER H 20 ASP H 21 0
SHEET 2 A 7 GLN H 156 PRO H 161 -1 O VAL H 157 N SER H 20
SHEET 3 A 7 LYS H 135 GLY H 140 -1 N VAL H 138 O VAL H 158
SHEET 4 A 7 PRO H 198 LYS H 202 -1 O VAL H 200 N ARG H 137
SHEET 5 A 7 TRP H 207 TRP H 215 -1 O TYR H 208 N MET H 201
SHEET 6 A 7 GLY H 226 HIS H 230 -1 O PHE H 227 N TRP H 215
SHEET 7 A 7 MET H 180 ALA H 183 -1 N PHE H 181 O TYR H 228
SHEET 1 B 7 GLN H 30 ARG H 35 0
SHEET 2 B 7 GLU H 39 LEU H 46 -1 O CYS H 42 N LEU H 33
SHEET 3 B 7 TRP H 51 THR H 54 -1 O LEU H 53 N SER H 45
SHEET 4 B 7 ALA H 104 LEU H 108 -1 O MET H 106 N VAL H 52
SHEET 5 B 7 LYS H 81 ILE H 90 -1 N TYR H 89 O LEU H 105
SHEET 6 B 7 LEU H 64 ILE H 68 -1 N VAL H 66 O SER H 83
SHEET 7 B 7 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65
SHEET 1 C 2 LEU H 60 TYR H 60A 0
SHEET 2 C 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 2.08
SSBOND 2 CYS H 42 CYS H 58 1555 1555 2.06
SSBOND 3 CYS H 168 CYS H 182 1555 1555 2.03
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.05
LINK NE2 HIS H 57 C3 0G6 H 301 1555 1555 1.39
LINK ND2 ASN H 60G C1 NAG H 302 1555 1555 1.46
LINK OG SER H 195 C2 0G6 H 301 1555 1555 1.38
LINK OD1 ASP L 1A ZN ZN L 101 1555 1555 1.77
LINK ZN ZN L 101 O HOH L 203 1555 1555 2.10
LINK ZN ZN L 101 NE2 HIS H 119 1555 1555 2.07
LINK OD1 ASP H 60E ZN ZN H 304 1555 1555 1.97
LINK OE2 GLU H 86 ZN ZN H 305 1555 1555 2.06
LINK O ARG H 221 NA NA H 303 1555 1555 2.35
LINK O LYS H 224 NA NA H 303 1555 1555 2.73
LINK NA NA H 303 O HOH H 428 1555 1555 3.00
LINK NA NA H 303 O HOH H 429 1555 1555 2.08
LINK NA NA H 303 O HOH H 437 1555 1555 2.53
LINK NA NA H 303 O HOH H 456 1555 1555 2.50
LINK ZN ZN H 305 O HOH H 402 1555 1555 2.28
LINK ZN ZN H 305 O HOH H 403 1555 1555 2.41
LINK ZN ZN H 305 O HOH H 523 1555 1555 2.45
LINK O6 DG D 1 NA B NA D 101 1555 1555 2.50
LINK O6 DG D 1 NA A NA D 101 1555 1555 2.72
LINK O6 DG D 2 NA A NA D 101 1555 1555 2.80
LINK O6 DG D 2 NA B NA D 101 1555 1555 3.12
LINK O6 DG D 5 NA A NA D 101 1555 1555 2.41
LINK O6 DG D 6 NA A NA D 101 1555 1555 2.74
LINK O6 DG D 6 NA B NA D 101 1555 1555 3.13
LINK O6 DG D 10 NA B NA D 101 1555 1555 2.71
LINK O6 DG D 10 NA A NA D 101 1555 1555 2.85
LINK O6 DG D 11 NA A NA D 101 1555 1555 2.63
LINK O6 DG D 11 NA B NA D 101 1555 1555 2.71
LINK O6 DG D 14 NA B NA D 101 1555 1555 2.60
LINK O6 DG D 14 NA A NA D 101 1555 1555 2.94
LINK O6 DG D 15 NA B NA D 101 1555 1555 2.16
LINK O6 DG D 15 NA A NA D 101 1555 1555 2.98
CISPEP 1 SER H 36A PRO H 37 0 -0.59
CRYST1 43.018 44.716 52.689 65.22 85.33 69.97 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 0.023246 -0.008475 0.001807 0.00000
SCALE2 0.000000 0.023803 -0.010947 0.00000
SCALE3 0.000000 0.000000 0.020960 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
