HEADER HYDROLASE 06-JAN-99 1B5F TITLE NATIVE CARDOSIN A FROM CYNARA CARDUNCULUS L. CAVEAT 1B5F BMA H 3 HAS WRONG CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (CARDOSIN A); COMPND 3 CHAIN: A, C; COMPND 4 EC: 3.4.23.-; COMPND 5 OTHER_DETAILS: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER COMPND 6 A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES COMPND 7 (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS COMPND 8 FROM THAT DEDUCED FROM CDNA THROUGH EXCISION OF THE PSI DOMAIN. COMPND 9 MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST- COMPND 10 TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES COMPND 11 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. COMPND 12 THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS COMPND 13 BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN COMPND 14 ASSIGNED CHAIN INDICATORS *C* AND *D*. MOLECULE 1 COMPOSED BY CHAINS COMPND 15 A(0-238) AND B (243-326). MOLECULE 2 COMPOSED BY CHAINS C(1-238) AND COMPND 16 D (243-326). N-LINKED CARBOHYDRATES (RESIDUES 401-405 A AND 401-406 COMPND 17 C) ATTACHED TO ASN 67. N-LINKED CARBOHYDRATES (RESIDUES 501-504 B AND COMPND 18 501-504 D) ATTACHED TO ASN 257.; COMPND 19 MOL_ID: 2; COMPND 20 MOLECULE: PROTEIN (CARDOSIN A); COMPND 21 CHAIN: B, D; COMPND 22 EC: 3.4.23.-; COMPND 23 OTHER_DETAILS: RESIDUE NAMES ACCORDING TO PEPSIN NUMBERING AFTER COMPND 24 A.R.SIELECKI, A.A.FEDOROV, A.BOODHOO, N.S.ANDREEVA, AND M.N.G.JAMES COMPND 25 (1990).J.MOL.BIOL. 214, 143-170. NATIVE CARDOSIN A SEQUENCE DIFFERS COMPND 26 FROM THAT DEDUCED FROM CDNA THROUGH EXCISION OF THE PSI DOMAIN. COMPND 27 MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A POST- COMPND 28 TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN COMPRISES RESIDUES COMPND 29 0/1 - 238 AND THE SECOND 15 KD CHAIN COMPRISES RESIDUES 243 - 326. COMPND 30 THE ASYMMETRIC UNIT CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS COMPND 31 BEEN ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 HAVE BEEN COMPND 32 ASSIGNED CHAIN INDICATORS *C* AND *D*. MOLECULE 1 COMPOSED BY CHAINS COMPND 33 A(0-238) AND B (243-326). MOLECULE 2 COMPOSED BY CHAINS C(1-238) AND COMPND 34 D (243-326). N-LINKED CARBOHYDRATES (RESIDUES 401-405 A AND 401-406 COMPND 35 C) ATTACHED TO ASN 67. N-LINKED CARBOHYDRATES (RESIDUES 501-504 B AND COMPND 36 501-504 D) ATTACHED TO ASN 257. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CYNARA CARDUNCULUS; SOURCE 3 ORGANISM_TAXID: 4265; SOURCE 4 ORGAN: FLOWER;PISTIL; SOURCE 5 TISSUE: PAPILLAR EPIDERMIS OF THE STIGMA; SOURCE 6 ORGANELLE: STORAGE VACUOLES; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: CYNARA CARDUNCULUS; SOURCE 9 ORGANISM_TAXID: 4265; SOURCE 10 ORGAN: FLOWER;PISTIL; SOURCE 11 TISSUE: PAPILLAR EPIDERMIS OF THE STIGMA; SOURCE 12 ORGANELLE: STORAGE VACUOLES KEYWDS HYDROLASE, ASPARTIC PROTEINASE EXPDTA X-RAY DIFFRACTION AUTHOR C.FRAZAO,I.BENTO,M.A.CARRONDO REVDAT 8 09-AUG-23 1B5F 1 REMARK REVDAT 7 23-SEP-20 1B5F 1 CAVEAT COMPND HETSYN LINK REVDAT 7 2 1 ATOM REVDAT 6 29-JUL-20 1B5F 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 13-JUL-11 1B5F 1 VERSN REVDAT 4 24-FEB-09 1B5F 1 VERSN REVDAT 3 01-APR-03 1B5F 1 JRNL REVDAT 2 29-DEC-99 1B5F 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 13-JAN-99 1B5F 0 JRNL AUTH C.FRAZAO,I.BENTO,J.COSTA,C.M.SOARES,P.VERISSIMO,C.FARO, JRNL AUTH 2 E.PIRES,J.COOPER,M.A.CARRONDO JRNL TITL CRYSTAL STRUCTURE OF CARDOSIN A, A GLYCOSYLATED AND JRNL TITL 2 ARG-GLY-ASP-CONTAINING ASPARTIC PROTEINASE FROM THE FLOWERS JRNL TITL 3 OF CYNARA CARDUNCULUS L. JRNL REF J.BIOL.CHEM. V. 274 27694 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 10488111 JRNL DOI 10.1074/JBC.274.39.27694 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH I.BENTO,C.FRAZAO,R.COELHO,K.WILSON,Z.DAUTER,M.A.CARRONDO REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 STUDIES OF THE PLANT ASPARTIC PROTEINASE CARDOSIN A REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 55 1465 1999 REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 AUTH I.BENTO,R.COELHO,C.FRAZAO,J.COSTA,C.FARO,P.VERISSIMO, REMARK 1 AUTH 2 E.PIRES,J.COOPER,Z.DAUTER,K.WILSON,M.A.CARRONDO REMARK 1 TITL CRYSTALLIZATION, STRUCTURE SOLUTION, AND INITIAL REFINEMENT REMARK 1 TITL 2 OF PLANT CARDOSIN-A REMARK 1 EDIT M.N.G.JAMES REMARK 1 REF ADV.EXP.MED.BIOL. V. 436 445 1998 REMARK 1 PUBL NEW YORK AND LONDON : PLENUM PRESS REMARK 1 REFN ISSN 0065-2598 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.206 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.205 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3994 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 83681 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.185 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.184 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3189 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 66752 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 229 REMARK 3 SOLVENT ATOMS : 528 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 5754.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 4964.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 18 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 23395 REMARK 3 NUMBER OF RESTRAINTS : 27500 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.040 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.045 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.021 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.069 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-2 REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: FUCOSE STEREOCHEMICAL TARGET PARAMETERS DERIVED REMARK 3 FROM 1.6 A RESOLUTION STRUCTURE PDB ENTRY 2MYR; REMARK 3 MANNOSE STEREOCHEMICAL TARGET PARAMETERS DERIVED REMARK 3 FROM 1.25 A RESOLUTION STRUCTURE PDB ENTRY 2WEA; N- REMARK 3 ACETYL-GLUCOSAMINE STEREOCHEMICAL TARGET REMARK 3 PARAMETERS DERIVED FROM 1.5 A STRUCTURE PDB ENTRY REMARK 3 1LZB REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, REMARK 3 J.APPL.CRYST.28 (1995)53-56. REMARK 3 DISORDERED REGIONS THAT WERE MODELED STEREOCHEMICALLY: 75-78 CHAIN REMARK 3 A AND 75-79 CHAIN C (FLAP); 46-46 REMARK 3 CHAIN A AND 46-47 CHAIN C; 159-160 AND 160B CHAIN A. REMARK 3 REMARK 3 DISORDERED REGIONS THAT WERE MODELED STEREOCHEMICALLY: REMARK 3 75-78 CHAIN A AND 75-79 CHAIN C (FLAP); 46-46 CHAIN A AND REMARK 3 46-47 CHAIN C; 159-160 AND 160B CHAIN A. REMARK 4 REMARK 4 1B5F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-APR-97 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9091 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 84399 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 34.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 11.30 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.41300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: HUMAN CATHEPSIN D (PDB ENTRY 1LYB)) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LYOPHILIZED PROTEIN DISSOLVED IN WATER REMARK 280 TO 12 MG/ML, SITTING DROPS OF PROTEIN SOLUTION AN ALIQUOTA OF REMARK 280 PRECIPITANT SOLUTION, COMPOSED OF PEG 4 K 40%, SODIUM CITRATE REMARK 280 BUFFER 0.1 M AND AMMONIUM ACETATE 0.2 M, PH 5.5 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 58.48200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.59300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 58.48200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.59300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, E, F 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, G, H 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH D 465 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 MATURE CARDOSIN A IS FOUND IN A TWO CHAIN FORM DUE TO A REMARK 400 POST-TRANSLATIONAL CLEAVAGE EVENT. A FIRST, 35 KD CHAIN REMARK 400 COMPRISES RESIDUES 0/1 - 238 AND THE SECOND 15 KD CHAIN REMARK 400 COMPRISES RESIDUES 243 - 326. THE ASYMMETRIC UNIT REMARK 400 CONTAINS TWO CARDOSIN A MOLECULES. MOLECULE 1 HAS BEEN REMARK 400 ASSIGNED CHAIN INDICATORS *A* AND *B*, AND MOLECULE 2 REMARK 400 HAVE BEEN ASSIGNED CHAIN INDICATORS *C* AND *D*. 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 GLY C 0 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 A 149 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 GLY C 204A C - N - CA ANGL. DEV. = 13.4 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 A 1 -25.58 -39.81 REMARK 500 ASP A 11 7.50 59.55 REMARK 500 LYS A 44 34.13 -90.75 REMARK 500 LYS A 44 37.75 -90.75 REMARK 500 CYS A 45 132.81 -37.94 REMARK 500 ASN A 67 -69.55 -131.19 REMARK 500 THR A 77 -54.62 -159.65 REMARK 500 HIS A 114 60.69 -108.97 REMARK 500 THR A 128 -86.09 -114.07 REMARK 500 TYR A 188 -65.74 -147.54 REMARK 500 LEU B 295 -33.27 78.38 REMARK 500 LYS C 44 27.77 -78.65 REMARK 500 ASN C 67 -64.18 -132.92 REMARK 500 TYR C 75 -171.54 -65.79 REMARK 500 THR C 77 -52.88 -151.79 REMARK 500 THR C 128 -85.35 -118.75 REMARK 500 GLU C 160A 30.33 -87.00 REMARK 500 TYR C 188 -63.10 -142.75 REMARK 500 LEU C 220 -167.13 -109.35 REMARK 500 GLU D 244 51.10 74.56 REMARK 500 LEU D 295 -50.96 73.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: 1 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: ASPARTIC PROTEINASE CATALYTIC SITE WATER 1014 REMARK 800 ASSOCIATED TO CHAIN A CATALYTIC SITE WATER 1035 ASSOCIATED TO REMARK 800 CHAIN C CATALYTIC SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: 2 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE ON CHAIN A, ASN67: (A1->3) REMARK 800 -MAN405 | ASN67-NAG401-(B1->4)-NAG403-(B1->4)-MAN404 | (A1->3) REMARK 800 FUC402 REMARK 800 REMARK 800 SITE_IDENTIFIER: 3 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE ON CHAIN B, ASN257: ASN257 REMARK 800 -NAG501-(B1->4)-NAG503-(B1->4)-MAN504 | (A1->3)-FUC502 REMARK 800 REMARK 800 SITE_IDENTIFIER: 4 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE ON CHAIN C, ASN67: (A1->3) REMARK 800 -MAN405 | ASN67-NAG401-(B1->4)-NAG403-(B1->4)-MAN404 | | (A1->3)- REMARK 800 FUC402 (A1->6)-MAN406 REMARK 800 REMARK 800 SITE_IDENTIFIER: 5 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: N-GLYCOSYLATION SITE ON CHAIN D, ASN257: ASN257 REMARK 800 -NAG501-(B1->4)-NAG503-(B1->4)-MAN504 | (A1->3)-FUC502 REMARK 800 REMARK 800 SITE_IDENTIFIER: 6 REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: NULL DBREF 1B5F A 0 238 EMBL CAB4134 AJ132884 71 309 DBREF 1B5F B 243 326 EMBL CAB4134 AJ132884 418 504 DBREF 1B5F C 0 238 EMBL CAB4134 AJ132884 71 309 DBREF 1B5F D 243 326 EMBL CAB4134 AJ132884 418 504 SEQRES 1 A 239 GLY SER ALA VAL VAL ALA LEU THR ASN ASP ARG ASP THR SEQRES 2 A 239 SER TYR PHE GLY GLU ILE GLY ILE GLY THR PRO PRO GLN SEQRES 3 A 239 LYS PHE THR VAL ILE PHE ASP THR GLY SER SER VAL LEU SEQRES 4 A 239 TRP VAL PRO SER SER LYS CYS ILE ASN SER LYS ALA CYS SEQRES 5 A 239 ARG ALA HIS SER MET TYR GLU SER SER ASP SER SER THR SEQRES 6 A 239 TYR LYS GLU ASN GLY THR PHE GLY ALA ILE ILE TYR GLY SEQRES 7 A 239 THR GLY SER ILE THR GLY PHE PHE SER GLN ASP SER VAL SEQRES 8 A 239 THR ILE GLY ASP LEU VAL VAL LYS GLU GLN ASP PHE ILE SEQRES 9 A 239 GLU ALA THR ASP GLU ALA ASP ASN VAL PHE LEU HIS ARG SEQRES 10 A 239 LEU PHE ASP GLY ILE LEU GLY LEU SER PHE GLN THR ILE SEQRES 11 A 239 SER VAL PRO VAL TRP TYR ASN MET LEU ASN GLN GLY LEU SEQRES 12 A 239 VAL LYS GLU ARG ARG PHE SER PHE TRP LEU ASN ARG ASN SEQRES 13 A 239 VAL ASP GLU GLU GLU GLY GLY GLU LEU VAL PHE GLY GLY SEQRES 14 A 239 LEU ASP PRO ASN HIS PHE ARG GLY ASP HIS THR TYR VAL SEQRES 15 A 239 PRO VAL THR TYR GLN TYR TYR TRP GLN PHE GLY ILE GLY SEQRES 16 A 239 ASP VAL LEU ILE GLY ASP LYS SER THR GLY PHE CYS ALA SEQRES 17 A 239 PRO GLY CYS GLN ALA PHE ALA ASP SER GLY THR SER LEU SEQRES 18 A 239 LEU SER GLY PRO THR ALA ILE VAL THR GLN ILE ASN HIS SEQRES 19 A 239 ALA ILE GLY ALA ASN SEQRES 1 B 87 GLU GLU LEU GLN VAL ASP CYS ASN THR LEU SER SER MET SEQRES 2 B 87 PRO ASN VAL SER PHE THR ILE GLY GLY LYS LYS PHE GLY SEQRES 3 B 87 LEU THR PRO GLU GLN TYR ILE LEU LYS VAL GLY LYS GLY SEQRES 4 B 87 GLU ALA THR GLN CYS ILE SER GLY PHE THR ALA MET ASP SEQRES 5 B 87 ALA THR LEU LEU GLY PRO LEU TRP ILE LEU GLY ASP VAL SEQRES 6 B 87 PHE MET ARG PRO TYR HIS THR VAL PHE ASP TYR GLY ASN SEQRES 7 B 87 LEU LEU VAL GLY PHE ALA GLU ALA ALA SEQRES 1 C 239 GLY SER ALA VAL VAL ALA LEU THR ASN ASP ARG ASP THR SEQRES 2 C 239 SER TYR PHE GLY GLU ILE GLY ILE GLY THR PRO PRO GLN SEQRES 3 C 239 LYS PHE THR VAL ILE PHE ASP THR GLY SER SER VAL LEU SEQRES 4 C 239 TRP VAL PRO SER SER LYS CYS ILE ASN SER LYS ALA CYS SEQRES 5 C 239 ARG ALA HIS SER MET TYR GLU SER SER ASP SER SER THR SEQRES 6 C 239 TYR LYS GLU ASN GLY THR PHE GLY ALA ILE ILE TYR GLY SEQRES 7 C 239 THR GLY SER ILE THR GLY PHE PHE SER GLN ASP SER VAL SEQRES 8 C 239 THR ILE GLY ASP LEU VAL VAL LYS GLU GLN ASP PHE ILE SEQRES 9 C 239 GLU ALA THR ASP GLU ALA ASP ASN VAL PHE LEU HIS ARG SEQRES 10 C 239 LEU PHE ASP GLY ILE LEU GLY LEU SER PHE GLN THR ILE SEQRES 11 C 239 SER VAL PRO VAL TRP TYR ASN MET LEU ASN GLN GLY LEU SEQRES 12 C 239 VAL LYS GLU ARG ARG PHE SER PHE TRP LEU ASN ARG ASN SEQRES 13 C 239 VAL ASP GLU GLU GLU GLY GLY GLU LEU VAL PHE GLY GLY SEQRES 14 C 239 LEU ASP PRO ASN HIS PHE ARG GLY ASP HIS THR TYR VAL SEQRES 15 C 239 PRO VAL THR TYR GLN TYR TYR TRP GLN PHE GLY ILE GLY SEQRES 16 C 239 ASP VAL LEU ILE GLY ASP LYS SER THR GLY PHE CYS ALA SEQRES 17 C 239 PRO GLY CYS GLN ALA PHE ALA ASP SER GLY THR SER LEU SEQRES 18 C 239 LEU SER GLY PRO THR ALA ILE VAL THR GLN ILE ASN HIS SEQRES 19 C 239 ALA ILE GLY ALA ASN SEQRES 1 D 87 GLU GLU LEU GLN VAL ASP CYS ASN THR LEU SER SER MET SEQRES 2 D 87 PRO ASN VAL SER PHE THR ILE GLY GLY LYS LYS PHE GLY SEQRES 3 D 87 LEU THR PRO GLU GLN TYR ILE LEU LYS VAL GLY LYS GLY SEQRES 4 D 87 GLU ALA THR GLN CYS ILE SER GLY PHE THR ALA MET ASP SEQRES 5 D 87 ALA THR LEU LEU GLY PRO LEU TRP ILE LEU GLY ASP VAL SEQRES 6 D 87 PHE MET ARG PRO TYR HIS THR VAL PHE ASP TYR GLY ASN SEQRES 7 D 87 LEU LEU VAL GLY PHE ALA GLU ALA ALA MODRES 1B5F ASN A 67 ASN GLYCOSYLATION SITE MODRES 1B5F ASN B 257 ASN GLYCOSYLATION SITE MODRES 1B5F ASN C 67 ASN GLYCOSYLATION SITE MODRES 1B5F ASN D 257 ASN GLYCOSYLATION SITE HET NAG E 1 14 HET NAG E 2 14 HET BMA E 3 11 HET MAN E 4 11 HET FUC E 5 10 HET NAG F 1 18 HET NAG F 2 14 HET BMA F 3 11 HET FUC F 4 10 HET NAG G 1 14 HET NAG G 2 14 HET BMA G 3 11 HET MAN G 4 11 HET MAN G 5 11 HET FUC G 6 10 HET NAG H 1 14 HET NAG H 2 14 HET BMA H 3 11 HET FUC H 4 20 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE 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 HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 5 NAG 8(C8 H15 N O6) FORMUL 5 BMA 4(C6 H12 O6) FORMUL 5 MAN 3(C6 H12 O6) FORMUL 5 FUC 4(C6 H12 O5) FORMUL 9 HOH *528(H2 O) HELIX 1 1 LYS A 48 ARG A 51 1 4 HELIX 2 2 SER A 58 ASP A 60 5 3 HELIX 3 3 ASP A 109 PHE A 112 1 4 HELIX 4 4 VAL A 136 ASN A 142 1 7 HELIX 5 5 PRO A 172 HIS A 174 5 3 HELIX 6 6 THR A 225 ALA A 234 1 10 HELIX 7 7 CYS B 249 SER B 254 5 6 HELIX 8 8 PRO B 271 TYR B 274 1 4 HELIX 9 9 ASP B 303 PRO B 308 1 6 HELIX 10 10 LYS C 48 ARG C 51 1 4 HELIX 11 11 SER C 58 ASP C 60 5 3 HELIX 12 12 ASP C 109 PHE C 112 1 4 HELIX 13 13 VAL C 136 ASN C 142 1 7 HELIX 14 14 PRO C 172 HIS C 174 5 3 HELIX 15 15 THR C 225 ILE C 235 1 11 HELIX 16 16 CYS D 249 SER D 254 5 6 HELIX 17 17 PRO D 271 TYR D 274 1 4 HELIX 18 18 ASP D 303 PRO D 308 1 6 SHEET 1 A 3 ALA A 2 LEU A 6 0 SHEET 2 A 3 GLY A 163 PHE A 167 -1 N PHE A 167 O ALA A 2 SHEET 3 A 3 PHE A 151 LEU A 155 -1 N TRP A 154 O GLU A 164 SHEET 1 B 4 THR A 7 ASP A 9 0 SHEET 2 B 4 SER A 13 ILE A 20 -1 N PHE A 15 O THR A 7 SHEET 3 B 4 GLN A 25 ASP A 32 -1 N VAL A 29 O GLY A 16 SHEET 4 B 4 GLY A 119 GLY A 122 1 N GLY A 119 O ILE A 30 SHEET 1 C 4 TRP A 39 PRO A 41 0 SHEET 2 C 4 GLN A 99 GLU A 107 1 N ILE A 102 O VAL A 40 SHEET 3 C 4 SER A 79 ASP A 87 -1 N ASP A 87 O GLN A 99 SHEET 4 C 4 PHE A 70 ILE A 74 -1 N ILE A 73 O ILE A 80 SHEET 1 D 2 VAL A 89 ILE A 91 0 SHEET 2 D 2 LEU A 94 VAL A 96 -1 N VAL A 96 O VAL A 89 SHEET 1 E 2 GLN A 191 ILE A 194 0 SHEET 2 E 2 CYS A 210 PHE A 213 -1 N ALA A 212 O PHE A 192 SHEET 1 F 2 VAL B 258 ILE B 262 0 SHEET 2 F 2 LYS B 265 LEU B 269 -1 N LEU B 269 O VAL B 258 SHEET 1 G 2 ILE B 275 VAL B 278 0 SHEET 2 G 2 GLN B 281 SER B 284 -1 N ILE B 283 O LEU B 276 SHEET 1 H 2 TYR B 309 ASP B 314 0 SHEET 2 H 2 LEU B 319 GLU B 324 -1 N ALA B 323 O HIS B 310 SHEET 1 I 3 ALA C 2 LEU C 6 0 SHEET 2 I 3 GLY C 163 PHE C 167 -1 N PHE C 167 O ALA C 2 SHEET 3 I 3 PHE C 151 LEU C 155 -1 N TRP C 154 O GLU C 164 SHEET 1 J 2 THR C 7 ASP C 9 0 SHEET 2 J 2 SER C 13 PHE C 15 -1 N PHE C 15 O THR C 7 SHEET 1 K 3 GLY C 16 ILE C 20 0 SHEET 2 K 3 GLN C 25 ASP C 32 -1 N VAL C 29 O GLY C 16 SHEET 3 K 3 GLY C 119 GLY C 122 1 N GLY C 119 O ILE C 30 SHEET 1 L 4 TRP C 39 PRO C 41 0 SHEET 2 L 4 GLN C 99 GLU C 107 1 N ILE C 102 O VAL C 40 SHEET 3 L 4 SER C 79 ASP C 87 -1 N ASP C 87 O GLN C 99 SHEET 4 L 4 PHE C 70 ILE C 74 -1 N ILE C 73 O ILE C 80 SHEET 1 M 2 VAL C 89 ILE C 91 0 SHEET 2 M 2 LEU C 94 VAL C 96 -1 N VAL C 96 O VAL C 89 SHEET 1 N 2 GLN C 191 ILE C 194 0 SHEET 2 N 2 CYS C 210 PHE C 213 -1 N ALA C 212 O PHE C 192 SHEET 1 O 2 VAL D 258 ILE D 262 0 SHEET 2 O 2 LYS D 265 LEU D 269 -1 N LEU D 269 O VAL D 258 SHEET 1 P 2 ILE D 275 VAL D 278 0 SHEET 2 P 2 GLN D 281 SER D 284 -1 N ILE D 283 O LEU D 276 SHEET 1 Q 2 TYR D 309 ASP D 314 0 SHEET 2 Q 2 LEU D 319 GLU D 324 -1 N ALA D 323 O HIS D 310 SSBOND 1 CYS A 45 CYS A 50 1555 1555 2.03 SSBOND 2 CYS A 206 CYS A 210 1555 1555 2.07 SSBOND 3 CYS B 249 CYS B 282 1555 1555 2.08 SSBOND 4 CYS C 45 CYS C 50 1555 1555 2.04 SSBOND 5 CYS C 206 CYS C 210 1555 1555 2.06 SSBOND 6 CYS D 249 CYS D 282 1555 1555 2.06 LINK ND2 ASN A 67 C1 NAG E 1 1555 1555 1.47 LINK ND2 ASN B 257 C1 NAG F 1 1555 1555 1.45 LINK ND2 ASN C 67 C1 NAG G 1 1555 1555 1.48 LINK ND2 ASN D 257 C1 NAG H 1 1555 1555 1.46 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.39 LINK O3 NAG E 1 C1 FUC E 5 1555 1555 1.43 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.40 LINK O3 BMA E 3 C1 MAN E 4 1555 1555 1.41 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.39 LINK O3 NAG F 1 C1 FUC F 4 1555 1555 1.43 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.39 LINK O4 NAG G 1 C1 NAG G 2 1555 1555 1.39 LINK O3 NAG G 1 C1 FUC G 6 1555 1555 1.43 LINK O4 NAG G 2 C1 BMA G 3 1555 1555 1.40 LINK O3 BMA G 3 C1 MAN G 4 1555 1555 1.41 LINK O6 BMA G 3 C1 MAN G 5 1555 1555 1.41 LINK O4 NAG H 1 C1 NAG H 2 1555 1555 1.39 LINK O3 NAG H 1 C1 AFUC H 4 1555 1555 1.42 LINK O3 NAG H 1 C1 BFUC H 4 1555 1555 1.42 LINK O4 NAG H 2 C1 BMA H 3 1555 1555 1.39 CISPEP 1 THR A 22 PRO A 23 0 -3.84 CISPEP 2 THR C 22 PRO C 23 0 1.24 SITE 1 1 2 ASP A 32 ASP A 215 SITE 1 2 1 ASN A 67 SITE 1 3 1 ASN B 257 SITE 1 4 2 ASP C 32 ASP C 215 SITE 1 5 1 ASN C 67 SITE 1 6 1 ASN D 257 CRYST1 116.964 87.186 81.303 90.00 104.43 90.00 C 1 2 1 8 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 0.008550 0.000000 0.002200 0.00000 SCALE2 0.000000 0.011470 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012700 0.00000 MTRIX1 1 -0.883650 -0.136860 0.447690 11.51360 1 MTRIX2 1 0.170040 -0.984830 0.034560 29.86930 1 MTRIX3 1 0.436170 0.106660 0.893520 -9.25410 1