HEADER HYDROLASE/HYDROLASE INHIBITOR 17-JUL-97 5GDS
TITLE HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE OF HUMAN
TITLE 2 ALPHA-THROMBIN:HIRUNORM V COMPLEX
CAVEAT 5GDS NAG H 400 HAS WRONG CHIRALITY AT ATOM C2 NAG H 400 HAS WRONG
CAVEAT 2 5GDS CHIRALITY AT ATOM C4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ALPHA-THROMBIN;
COMPND 3 CHAIN: L;
COMPND 4 EC: 3.4.21.5;
COMPND 5 MOL_ID: 2;
COMPND 6 MOLECULE: ALPHA-THROMBIN;
COMPND 7 CHAIN: H;
COMPND 8 EC: 3.4.21.5;
COMPND 9 MOL_ID: 3;
COMPND 10 MOLECULE: HIRUNORM V;
COMPND 11 CHAIN: I;
COMPND 12 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 ORGAN: BLOOD;
SOURCE 6 TISSUE: PLASMA;
SOURCE 7 MOL_ID: 2;
SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 9 ORGANISM_COMMON: HUMAN;
SOURCE 10 ORGANISM_TAXID: 9606;
SOURCE 11 ORGAN: BLOOD;
SOURCE 12 TISSUE: PLASMA;
SOURCE 13 MOL_ID: 3
KEYWDS SERINE PROTEASE-INHIBITOR COMPLEX, THROMBIN, THROMBIN SYNTHETIC
KEYWDS 2 INHIBITORS, ANTITHROMBOTICS, HIRUNORMS, HIRUDIN-LIKE BINDING MODE,
KEYWDS 3 BLOOD COAGULATION, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR G.DE SIMONE,A.LOMBARDI,S.GALDIERO,F.NASTRI,R.DELLA MORTE,N.STAIANO,
AUTHOR 2 C.PEDONE,M.BOLOGNESI,V.PAVONE
REVDAT 5 09-AUG-23 5GDS 1 REMARK HETSYN
REVDAT 4 29-JUL-20 5GDS 1 CAVEAT COMPND REMARK HETNAM
REVDAT 4 2 1 LINK SITE
REVDAT 3 13-JUL-11 5GDS 1 VERSN
REVDAT 2 24-FEB-09 5GDS 1 VERSN
REVDAT 1 21-JAN-98 5GDS 0
JRNL AUTH G.DE SIMONE,A.LOMBARDI,S.GALDIERO,F.NASTRI,R.DELLA MORTE,
JRNL AUTH 2 N.STAIANO,C.PEDONE,M.BOLOGNESI,V.PAVONE
JRNL TITL HIRUNORMS ARE TRUE HIRUDIN MIMETICS. THE CRYSTAL STRUCTURE
JRNL TITL 2 OF HUMAN ALPHA-THROMBIN-HIRUNORM V COMPLEX.
JRNL REF PROTEIN SCI. V. 7 243 1998
JRNL REFN ISSN 0961-8368
JRNL PMID 9521099
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH A.LOMBARDI,F.NASTRI,R.DELLA MORTE,A.ROSSI,A.DE ROSA,
REMARK 1 AUTH 2 N.STAIANO,C.PEDONE,V.PAVONE
REMARK 1 TITL RATIONAL DESIGN OF TRUE HIRUDIN MIMETICS: SYNTHESIS AND
REMARK 1 TITL 2 CHARACTERIZATION OF MULTISITE-DIRECTED ALPHA-THROMBIN
REMARK 1 TITL 3 INHIBITORS
REMARK 1 REF J.MED.CHEM. V. 39 2008 1996
REMARK 1 REFN ISSN 0022-2623
REMARK 1 REFERENCE 2
REMARK 1 AUTH T.J.RYDEL,A.TULINSKY,W.BODE,R.HUBER
REMARK 1 TITL REFINED STRUCTURE OF THE HIRUDIN-THROMBIN COMPLEX
REMARK 1 REF J.MOL.BIOL. V. 221 583 1991
REMARK 1 REFN ISSN 0022-2836
REMARK 2
REMARK 2 RESOLUTION. 2.10 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : TNT 5E
REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 97.0
REMARK 3 NUMBER OF REFLECTIONS : 21609
REMARK 3
REMARK 3 USING DATA ABOVE SIGMA CUTOFF.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : NULL
REMARK 3 R VALUE (WORKING SET) : 0.176
REMARK 3 FREE R VALUE : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 USING ALL DATA, NO SIGMA CUTOFF.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1760
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 21609
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2476
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 14
REMARK 3 SOLVENT ATOMS : 133
REMARK 3
REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : 28.700
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT
REMARK 3 BOND LENGTHS (A) : 0.018 ; 18.000; 3483
REMARK 3 BOND ANGLES (DEGREES) : 2.800 ; 40.000; 3474
REMARK 3 TORSION ANGLES (DEGREES) : 17.835; 7.000 ; 1503
REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL
REMARK 3 TRIGONAL CARBON PLANES (A) : 0.021 ; 29.000; 62
REMARK 3 GENERAL PLANES (A) : 0.021 ; 99.000; 362
REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS (A) : 0.230 ; 25.000; 81
REMARK 3
REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : 0.83
REMARK 3 BSOL : 158.7
REMARK 3
REMARK 3 RESTRAINT LIBRARIES.
REMARK 3 STEREOCHEMISTRY : NULL
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE REGIONS WITH INTERRUPTED ELECTRON DENSITIES ARE FOUND
REMARK 3 IN THE N-TERMINAL AND C-TERMINAL REGIONS OF CHAIN L, THE
REMARK 3 C-TERMINAL REGION OF CHAIN H, AND SOME RESIDUES IN THE
REMARK 3 AUTOLYSIS LOOP. THESE REGIONS INCLUDE: THR L 1H -
REMARK 3 GLU L 1C; ASP L 14L - ARG L 15; THR H 147 AND TRP H 148;
REMARK 3 GLY H 246 AND GLU H 247. RESIDUES THR H 149 - LYS H 149E
REMARK 3 IN THE GAMMA AUTOLYSIS LOOP ARE FOUND WITH NO ELECTRON
REMARK 3 DENSITIES AND ARE NOT INCLUDED IN THIS ENTRY. THERE IS
REMARK 3 NO ELECTRON DENSITY FOT HIRUNORM V RESIDUES I 5 - I 15.
REMARK 3 OTHER ATOMS WITH NO DENSITY ARE GIVEN OCCUPANCY VALUES OF
REMARK 3 0.00 IN THIS ENTRY.
REMARK 4
REMARK 4 5GDS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000179714.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 10-JAN-96
REMARK 200 TEMPERATURE (KELVIN) : 293
REMARK 200 PH : 7.0
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 RUH2R
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : COLLIMATOR
REMARK 200
REMARK 200 DETECTOR TYPE : IMAGE PLATE
REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, CCP4
REMARK 200 DATA SCALING SOFTWARE : CCP4
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21615
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4
REMARK 200 DATA REDUNDANCY : 2.500
REMARK 200 R MERGE (I) : 0.07200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17
REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7
REMARK 200 DATA REDUNDANCY IN SHELL : 2.50
REMARK 200 R MERGE FOR SHELL (I) : 0.38000
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: THE STRUCTURE WAS ANALYZED
REMARK 200 BY DIFFERENCE FOURIER TECHNIQUES
REMARK 200 SOFTWARE USED: CCP4
REMARK 200 STARTING MODEL: PDB ENTRY 1HAH (J. VIJAYALAKSHMI ET AL., 1994,
REMARK 200 PROTEIN SCI. 3,2254-71)
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 49.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: THE CRYSTALS OF THROMBIN:HIRUNORM V
REMARK 280 COMPLEX WERE GROWN, AS DESCRIBED BY SKRZYPEZAK ET AL. (1991) J.
REMARK 280 MOL. BIOL.,221,1379-1393 BY VAPOR DIFFUSION METHODS AT 4 C. A 6
REMARK 280 MICROLITER DROP, CONTAINING 0.05 M SODIUM HEPES (PH 7.0) 10% (W/
REMARK 280 V) PEG 4000 0.02% NAN3, 20 MG/ML. THROMBIN:HIRUNORM V COMPLEX
REMARK 280 WAS EQUILIBRATED AGAINST A PRECIPITATING SOLUTION CONTAINING 0.1
REMARK 280 M SODIUM HEPES (PH 7.0) 20% (W/V) PEG 4000 0.04% NAN3. CRYSTAL
REMARK 280 OF THROMBIN:HIRUGEN COMPLEX WERE CRUSHED AND INDIVIDUAL SEEDS
REMARK 280 WERE USED FOR CROSS-SEEDING EXPERIMENTS., VAPOR DIFFUSION,
REMARK 280 TEMPERATURE 277K
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 35.95000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.40000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 35.95000
REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 36.40000
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: 5780 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 13150 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: L, H, I
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 400
REMARK 400 COMPOUND
REMARK 400 THROMBIN IS CLEAVED BETWEEN RESIDUES 15 AND 16. CHAIN
REMARK 400 INDICATOR *L* IS USED FOR RESIDUES 1H - 15 AND CHAIN
REMARK 400 INDICATOR *H* IS USED FOR RESIDUES 16 - 247. CHAIN
REMARK 400 INDICATOR *I* IS USED FOR HIRUNORM V INHIBITOR.
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 H 148A
REMARK 465 ALA H 148B
REMARK 465 ASN H 148C
REMARK 465 VAL H 148D
REMARK 465 GLY H 148E
REMARK 465 LYS H 148F
REMARK 465 ASP I 5
REMARK 465 DAL I 6
REMARK 465 GLY I 7
REMARK 465 BAL I 8
REMARK 465 PRO I 9
REMARK 465 GLU I 10
REMARK 465 SER I 11
REMARK 465 HIS I 12
REMARK 465 HMF I 13
REMARK 465 GLY I 14
REMARK 465 GLY I 15
REMARK 475
REMARK 475 ZERO OCCUPANCY RESIDUES
REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY.
REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT
REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE)
REMARK 475 M RES C SSEQI
REMARK 475 THR L 1H
REMARK 475 PHE L 1G
REMARK 475 GLY L 1F
REMARK 475 SER L 1E
REMARK 475 GLY L 1D
REMARK 475 ASP L 14L
REMARK 475 GLY L 14M
REMARK 475 ARG L 15
REMARK 475 TRP H 148
REMARK 475 GLU H 247
REMARK 475 TYR I 24
REMARK 475 ALC I 25
REMARK 475 DGL I 26
REMARK 480
REMARK 480 ZERO OCCUPANCY ATOM
REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 480 M RES C SSEQI ATOMS
REMARK 480 GLU L 1C CB CG CD OE1 OE2
REMARK 480 GLU L 13 CD OE1 OE2
REMARK 480 LYS L 14A CG CD CE NZ
REMARK 480 ARG L 14D CD NE CZ NH1 NH2
REMARK 480 GLU L 14H OE1 OE2
REMARK 480 ILE L 14K C O
REMARK 480 GLU H 18 CD OE1 OE2
REMARK 480 SER H 36A CB OG
REMARK 480 GLN H 38 CD OE1 NE2
REMARK 480 GLU H 39 CD OE1 OE2
REMARK 480 ARG H 50 CG CD NE CZ NH1 NH2
REMARK 480 ASN H 62 CG OD1 ND2
REMARK 480 LYS H 81 CD CE NZ
REMARK 480 GLU H 86 OE1 OE2
REMARK 480 LYS H 87 CD CE NZ
REMARK 480 LYS H 107 CE NZ
REMARK 480 LYS H 109 CE NZ
REMARK 480 LYS H 110 CG CD CE NZ
REMARK 480 ARG H 126 CD NE CZ NH1 NH2
REMARK 480 GLU H 127 CG CD OE1 OE2
REMARK 480 GLN H 131 OE1 NE2
REMARK 480 LYS H 145 CE NZ
REMARK 480 THR H 147 O CB OG1 CG2
REMARK 480 GLY H 150 N
REMARK 480 GLN H 151 CG CD OE1 NE2
REMARK 480 LYS H 169 CD CE NZ
REMARK 480 ASP H 186A CG OD1 OD2
REMARK 480 LYS H 186D CD CE NZ
REMARK 480 GLU H 192 CD OE1 OE2
REMARK 480 ASN H 205 OD1 ND2
REMARK 480 ARG H 233 CZ NH1
REMARK 480 LYS H 235 NZ
REMARK 480 LYS H 236 CG CD CE NZ
REMARK 480 TRP H 237 N
REMARK 480 GLN H 239 CG CD OE1 NE2
REMARK 480 LYS H 240 CD CE NZ
REMARK 480 ASP H 243 CG OD1 OD2
REMARK 480 GLN H 244 CD OE1 NE2
REMARK 480 GLY H 246 C O
REMARK 480 GLU I 19 CD OE1 OE2
REMARK 480 AIB I 22 CB1
REMARK 480 AIB I 23 O CB1 CB2
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 N GLU H 146 O HOH H 523 2.12
REMARK 500 ND2 ASN H 60G O5 NAG H 400 2.16
REMARK 500 ND2 ASN H 60G C2 NAG H 400 2.17
REMARK 500 CG ASN H 60G C1 NAG H 400 2.18
REMARK 500 O HOH H 403 O HOH H 462 2.18
REMARK 500
REMARK 500 REMARK: NULL
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 O ASP L 14L NH2 ARG H 173 4556 1.75
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 GLU L 8 CD GLU L 8 OE2 0.068
REMARK 500 GLU L 14C CD GLU L 14C OE2 0.083
REMARK 500 GLU H 23 CD GLU H 23 OE2 0.075
REMARK 500 GLU H 61 CD GLU H 61 OE2 0.099
REMARK 500 ARG H 75 CB ARG H 75 CG 0.174
REMARK 500 GLU H 80 CD GLU H 80 OE1 0.072
REMARK 500 GLU H 97A CD GLU H 97A OE2 0.090
REMARK 500 GLU H 164 CD GLU H 164 OE2 0.078
REMARK 500 GLU H 217 CD GLU H 217 OE2 0.072
REMARK 500 GLU I 18 CD GLU I 18 OE2 0.087
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 ASP L 1A CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES
REMARK 500 ASP L 14 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 ASP L 14 CB - CG - OD2 ANGL. DEV. = -6.4 DEGREES
REMARK 500 SER H 27 N - CA - CB ANGL. DEV. = 11.5 DEGREES
REMARK 500 ASP H 49 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES
REMARK 500 ASP H 49 CB - CG - OD2 ANGL. DEV. = -8.5 DEGREES
REMARK 500 ASP H 60E CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES
REMARK 500 ARG H 77A NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES
REMARK 500 ARG H 77A NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES
REMARK 500 ARG H 93 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 ARG H 97 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES
REMARK 500 ARG H 97 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES
REMARK 500 ASP H 100 CB - CG - OD1 ANGL. DEV. = 7.5 DEGREES
REMARK 500 ASP H 100 CB - CG - OD2 ANGL. DEV. = -9.0 DEGREES
REMARK 500 ARG H 101 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES
REMARK 500 ARG H 101 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES
REMARK 500 ASP H 102 CB - CG - OD2 ANGL. DEV. = -8.5 DEGREES
REMARK 500 ASP H 125 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES
REMARK 500 ASP H 125 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES
REMARK 500 ASP H 170 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES
REMARK 500 ASP H 186A CB - CG - OD1 ANGL. DEV. = -5.4 DEGREES
REMARK 500 ARG H 206 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES
REMARK 500 ARG H 206 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 ASP H 221 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES
REMARK 500 ARG H 221A NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES
REMARK 500 ASP I 16 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES
REMARK 500 PRO I 21 C - N - CA ANGL. DEV. = 9.1 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 SER L 1E 5.63 51.99
REMARK 500 PHE L 7 -84.68 -130.23
REMARK 500 TYR L 14J 24.28 -79.04
REMARK 500 ILE L 14K 31.63 70.78
REMARK 500 ASP L 14L 104.12 93.59
REMARK 500 TYR H 60A 75.00 -159.11
REMARK 500 HIS H 71 -60.04 -133.75
REMARK 500 GLU H 77 80.79 -69.09
REMARK 500 GLU H 97A -63.77 -132.99
REMARK 500 LYS H 186D 132.00 -170.53
REMARK 500 TYR I 24 -38.59 -16.96
REMARK 500 ALC I 25 -89.08 -58.19
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 GLN H 156 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 615
REMARK 615 ZERO OCCUPANCY ATOM
REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO
REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS
REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME;
REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE):
REMARK 615 M RES C SSEQI
REMARK 615 NAG H 400
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: CAT
REMARK 800 EVIDENCE_CODE: UNKNOWN
REMARK 800 SITE_DESCRIPTION: CATALYTIC SITE.
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 CHYMOTRYPSIN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS
REMARK 999 USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE
REMARK 999 STRUCTURE OF CHYMOTRYPSIN (W.BODE ET AL., 1989, EMBO J. 8,
REMARK 999 3467-3475).
DBREF 5GDS L 1 15 UNP P00734 THRB_HUMAN 328 363
DBREF 5GDS H 16 247 UNP P00734 THRB_HUMAN 364 622
DBREF 5GDS I 1 26 PDB 5GDS 5GDS 1 26
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 I 26 CHG VAL NAL THR ASP DAL GLY BAL PRO GLU SER HIS HMF
SEQRES 2 I 26 GLY GLY ASP TYR GLU GLU ILE PRO AIB AIB TYR ALC DGL
MODRES 5GDS ASN H 60G ASN GLYCOSYLATION SITE
MODRES 5GDS NAL I 3 ALA BETA-(2-NAPHTHYL)-ALANINE
MODRES 5GDS AIB I 22 ALA ALPHA-AMINOISOBUTYRIC ACID
MODRES 5GDS AIB I 23 ALA ALPHA-AMINOISOBUTYRIC ACID
MODRES 5GDS ALC I 25 ALA 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
HET CHG I 1 10
HET NAL I 3 15
HET AIB I 22 6
HET AIB I 23 6
HET ALC I 25 10
HET DGL I 26 10
HET NAG H 400 14
HETNAM CHG CYCLOHEXYL-GLYCINE
HETNAM NAL BETA-(2-NAPHTHYL)-ALANINE
HETNAM AIB ALPHA-AMINOISOBUTYRIC ACID
HETNAM ALC 2-AMINO-3-CYCLOHEXYL-PROPIONIC ACID
HETNAM DGL D-GLUTAMIC ACID
HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE
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 3 CHG C8 H15 N O2
FORMUL 3 NAL C13 H13 N O2
FORMUL 3 AIB 2(C4 H9 N O2)
FORMUL 3 ALC C9 H17 N O2
FORMUL 3 DGL C5 H9 N O4
FORMUL 4 NAG C8 H15 N O6
FORMUL 5 HOH *133(H2 O)
HELIX 1 1 GLU L 8 LYS L 10 5 3
HELIX 2 2 GLU L 14C SER L 14I 1 7
HELIX 3 3 ALA H 56 CYS H 58 5 3
HELIX 4 4 PRO H 60B TRP H 60D 5 3
HELIX 5 5 GLU H 61 ASP H 63 5 3
HELIX 6 6 ARG H 126 LEU H 129C 1 7
HELIX 7 7 ARG H 165 SER H 171 1 7
HELIX 8 8 PRO H 186 GLU H 186B 5 3
HELIX 9 9 PHE H 232 PHE H 245 5 14
SHEET 1 A 4 LYS H 81 MET H 84 0
SHEET 2 A 4 LEU H 64 ILE H 68 -1 N ILE H 68 O LYS H 81
SHEET 3 A 4 GLN H 30 ARG H 35 -1 N PHE H 34 O LEU H 65
SHEET 4 A 4 GLU H 39 SER H 45 -1 N ALA H 44 O VAL H 31
SHEET 1 B 3 TRP H 51 THR H 54 0
SHEET 2 B 3 ALA H 104 LEU H 108 -1 N MET H 106 O VAL H 52
SHEET 3 B 3 LEU H 85 ILE H 90 -1 N TYR H 89 O LEU H 105
SHEET 1 C 2 LYS H 135 GLY H 140 0
SHEET 2 C 2 GLN H 156 PRO H 161 -1 N LEU H 160 O GLY H 136
SHEET 1 D 4 MET H 180 ALA H 183 0
SHEET 2 D 4 GLY H 226 HIS H 230 -1 N TYR H 228 O PHE H 181
SHEET 3 D 4 TRP H 207 TRP H 215 -1 N TRP H 215 O PHE H 227
SHEET 4 D 4 PRO H 198 LYS H 202 -1 N MET H 201 O TYR H 208
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 2.02
SSBOND 4 CYS H 191 CYS H 220 1555 1555 2.06
LINK ND2 ASN H 60G C1 NAG H 400 1555 1555 1.39
LINK C CHG I 1 N VAL I 2 1555 1555 1.34
LINK C VAL I 2 N NAL I 3 1555 1555 1.34
LINK C PRO I 21 N AIB I 22 1555 1555 1.35
LINK C AIB I 22 N AIB I 23 1555 1555 1.33
LINK C AIB I 23 N TYR I 24 1555 1555 1.34
LINK C TYR I 24 N ALC I 25 1555 1555 1.32
LINK C ALC I 25 N DGL I 26 1555 1555 1.33
CISPEP 1 SER H 36A PRO H 37 0 2.86
SITE 1 CAT 3 HIS H 57 ASP H 102 SER H 195
CRYST1 71.900 72.800 73.300 90.00 100.70 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 0.013908 0.000000 0.002628 0.00000
SCALE2 0.000000 0.013736 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013884 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
