PDB Short entry for 1LYA HEADER LYSOSOMAL ASPARTIC PROTEASE 22-APR-93 1LYA TITLE CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN CATHEPSIN D: TITLE 2 IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG DESIGN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATHEPSIN D; COMPND 3 CHAIN: A, C; COMPND 4 EC: 3.4.23.5; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: CATHEPSIN D; COMPND 7 CHAIN: B, D; COMPND 8 EC: 3.4.23.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 ORGAN: LIVER; SOURCE 6 TISSUE: LIVER; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 ORGAN: LIVER; SOURCE 12 TISSUE: LIVER KEYWDS LYSOSOMAL ASPARTIC PROTEASE EXPDTA X-RAY DIFFRACTION AUTHOR E.T.BALDWIN,T.N.BHAT,S.GULNIK,J.W.ERICKSON REVDAT 6 29-JUL-20 1LYA 1 COMPND REMARK HETNAM LINK REVDAT 6 2 1 SITE ATOM REVDAT 5 29-NOV-17 1LYA 1 HELIX REVDAT 4 13-JUL-11 1LYA 1 VERSN REVDAT 3 24-FEB-09 1LYA 1 VERSN REVDAT 2 01-APR-03 1LYA 1 JRNL REVDAT 1 31-JAN-94 1LYA 0 JRNL AUTH E.T.BALDWIN,T.N.BHAT,S.GULNIK,M.V.HOSUR,R.C.SOWDER 2ND., JRNL AUTH 2 R.E.CACHAU,J.COLLINS,A.M.SILVA,J.W.ERICKSON JRNL TITL CRYSTAL STRUCTURES OF NATIVE AND INHIBITED FORMS OF HUMAN JRNL TITL 2 CATHEPSIN D: IMPLICATIONS FOR LYSOSOMAL TARGETING AND DRUG JRNL TITL 3 DESIGN. JRNL REF PROC.NATL.ACAD.SCI.USA V. 90 6796 1993 JRNL REFN ISSN 0027-8424 JRNL PMID 8393577 JRNL DOI 10.1073/PNAS.90.14.6796 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.GULNIK,E.T.BALDWIN,N.TARASOVA,J.ERICKSON REMARK 1 TITL HUMAN LIVER CATHEPSIN D. PURIFICATION, CRYSTALLIZATION AND REMARK 1 TITL 2 PRELIMINARY X-RAY DIFFRACTION ANALYSIS OF A LYSOSOMAL ENZYME REMARK 1 REF J.MOL.BIOL. V. 227 265 1992 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.0 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL 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 : 28077 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.188 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 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 : 5186 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 128 REMARK 3 SOLVENT ATOMS : 46 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) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 3.100 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; 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: REMARK 3 THERE ARE TWO N-LINKED OLIGOSACCHARIDES ATTACHED AT REMARK 3 RESIDUES ASN 70 AND ASN 199 OF EACH MOLECULE. FOUR SUGARS REMARK 3 WERE INCLUDED FOR REFINEMENT AT ASN 70 AND A SINGLE REMARK 3 N-LINKED NAG AT ASN 199. THE SUGARS ARE LINKED AS FOLLOWS: REMARK 3 REMARK 3 ASN A 70 -- NAG A 1 -- NAG A 2 -- MAN A 3 -- MAN A 8 REMARK 3 ASN B 199 -- NAG B 1 REMARK 3 ASN C 70 -- NAG C 1 -- NAG C 2 -- MAN C 3 -- MAN C 8 REMARK 3 ASN D 199 -- NAG D 1 REMARK 4 REMARK 4 1LYA 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_1000174856. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR 3.0 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.40000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.70000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 52.05000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 17.35000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 86.75000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL REMARK 300 YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN REMARK 300 APPLIED TO CHAINS *C* AND *D*, RESPECTIVELY. 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 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: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -66.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 APPLY THE FOLLOWING TO CHAINS: C, D, F REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 62.95000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 109.03260 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 -34.70000 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 GLN A 97 CG CD OE1 NE2 REMARK 470 GLN C 97 CG CD OE1 NE2 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 HD22 ASN C 60 HZ2 LYS C 63 1.28 REMARK 500 HH TYR C 15 HH21 ARG D 171 1.33 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 HIS A 45 NE2 HIS A 45 CD2 -0.068 REMARK 500 HIS A 56 NE2 HIS A 56 CD2 -0.072 REMARK 500 HIS A 57 NE2 HIS A 57 CD2 -0.072 REMARK 500 HIS C 45 NE2 HIS C 45 CD2 -0.068 REMARK 500 HIS C 56 NE2 HIS C 56 CD2 -0.066 REMARK 500 HIS C 57 NE2 HIS C 57 CD2 -0.070 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 TRP A 40 CD1 - CG - CD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 TRP A 40 CB - CG - CD1 ANGL. DEV. = -8.2 DEGREES REMARK 500 TRP A 40 CE2 - CD2 - CG ANGL. DEV. = -6.3 DEGREES REMARK 500 TRP A 40 CG - CD2 - CE3 ANGL. DEV. = 5.5 DEGREES REMARK 500 TRP A 54 CD1 - CG - CD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 TRP A 54 CG - CD1 - NE1 ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP A 54 CE2 - CD2 - CG ANGL. DEV. = -5.4 DEGREES REMARK 500 TYR A 59 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 TRP B 206 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP B 206 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 LEU B 247 CA - CB - CG ANGL. DEV. = 14.8 DEGREES REMARK 500 ALA B 297 N - CA - C ANGL. DEV. = -20.6 DEGREES REMARK 500 TRP B 319 CD1 - CG - CD2 ANGL. DEV. = 6.4 DEGREES REMARK 500 TRP B 319 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 335 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 339 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TRP C 40 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP C 40 CE2 - CD2 - CG ANGL. DEV. = -5.9 DEGREES REMARK 500 TRP C 54 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP C 54 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 LEU C 83 CA - CB - CG ANGL. DEV. = 20.0 DEGREES REMARK 500 ARG D 112 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 MET D 182 CA - CB - CG ANGL. DEV. = -11.6 DEGREES REMARK 500 TRP D 206 CD1 - CG - CD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 TRP D 206 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 MET D 237 CG - SD - CE ANGL. DEV. = -10.8 DEGREES REMARK 500 TRP D 319 CD1 - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TRP D 319 CE2 - CD2 - CG ANGL. DEV. = -5.7 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 ASP A 12 18.67 58.36 REMARK 500 HIS A 45 31.17 -98.82 REMARK 500 ASN A 70 -50.09 -135.82 REMARK 500 SER A 80 -76.01 168.20 REMARK 500 PRO A 95 -143.14 -66.04 REMARK 500 THR B 201 -79.05 -83.69 REMARK 500 ALA B 204 -67.05 -144.25 REMARK 500 ALA B 216 -18.20 -45.61 REMARK 500 CYS B 222 28.85 49.60 REMARK 500 GLU B 224 -18.10 107.20 REMARK 500 LEU B 256 -71.58 -94.55 REMARK 500 ILE B 257 143.60 -171.95 REMARK 500 GLN B 296 -55.63 -159.24 REMARK 500 ALA B 297 -71.12 -89.09 REMARK 500 LYS B 299 -170.96 52.39 REMARK 500 THR B 300 -6.50 54.82 REMARK 500 ASN C 70 -77.35 -126.69 REMARK 500 SER C 80 -89.03 178.09 REMARK 500 PRO C 95 -177.29 -67.71 REMARK 500 ASP D 174 -38.94 -165.74 REMARK 500 ALA D 204 -68.10 -124.24 REMARK 500 ALA D 216 -35.83 -35.75 REMARK 500 GLU D 224 -24.20 72.00 REMARK 500 LEU D 256 -82.30 -102.07 REMARK 500 GLN D 258 74.76 35.95 REMARK 500 ALA D 297 -137.70 62.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO D 313 PRO D 314 36.80 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. REMARK 700 THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE REMARK 700 IDENTICAL STRANDS. SHEETS *1A1* AND *1B1* AND SHEETS *1A2* REMARK 700 AND *1B2* REPRESENT ONE BIFURCATED SHEET IN EACH MOLECULE. REMARK 700 SHEETS *2A1* AND *2B1* AND *2A2* AND *2B2* REPRESENT ONE REMARK 700 BIFURCATED SHEET IN EACH MOLECULE. DBREF 1LYA A 1 97 UNP P07339 CATD_HUMAN 65 161 DBREF 1LYA B 106 346 UNP P07339 CATD_HUMAN 170 410 DBREF 1LYA C 1 97 UNP P07339 CATD_HUMAN 65 161 DBREF 1LYA D 106 346 UNP P07339 CATD_HUMAN 170 410 SEQRES 1 A 97 GLY PRO ILE PRO GLU VAL LEU LYS ASN TYR MET ASP ALA SEQRES 2 A 97 GLN TYR TYR GLY GLU ILE GLY ILE GLY THR PRO PRO GLN SEQRES 3 A 97 CYS PHE THR VAL VAL PHE ASP THR GLY SER SER ASN LEU SEQRES 4 A 97 TRP VAL PRO SER ILE HIS CYS LYS LEU LEU ASP ILE ALA SEQRES 5 A 97 CYS TRP ILE HIS HIS LYS TYR ASN SER ASP LYS SER SER SEQRES 6 A 97 THR TYR VAL LYS ASN GLY THR SER PHE ASP ILE HIS TYR SEQRES 7 A 97 GLY SER GLY SER LEU SER GLY TYR LEU SER GLN ASP THR SEQRES 8 A 97 VAL SER VAL PRO CYS GLN SEQRES 1 B 241 GLY GLY VAL LYS VAL GLU ARG GLN VAL PHE GLY GLU ALA SEQRES 2 B 241 THR LYS GLN PRO GLY ILE THR PHE ILE ALA ALA LYS PHE SEQRES 3 B 241 ASP GLY ILE LEU GLY MET ALA TYR PRO ARG ILE SER VAL SEQRES 4 B 241 ASN ASN VAL LEU PRO VAL PHE ASP ASN LEU MET GLN GLN SEQRES 5 B 241 LYS LEU VAL ASP GLN ASN ILE PHE SER PHE TYR LEU SER SEQRES 6 B 241 ARG ASP PRO ASP ALA GLN PRO GLY GLY GLU LEU MET LEU SEQRES 7 B 241 GLY GLY THR ASP SER LYS TYR TYR LYS GLY SER LEU SER SEQRES 8 B 241 TYR LEU ASN VAL THR ARG LYS ALA TYR TRP GLN VAL HIS SEQRES 9 B 241 LEU ASP GLN VAL GLU VAL ALA SER GLY LEU THR LEU CYS SEQRES 10 B 241 LYS GLU GLY CYS GLU ALA ILE VAL ASP THR GLY THR SER SEQRES 11 B 241 LEU MET VAL GLY PRO VAL ASP GLU VAL ARG GLU LEU GLN SEQRES 12 B 241 LYS ALA ILE GLY ALA VAL PRO LEU ILE GLN GLY GLU TYR SEQRES 13 B 241 MET ILE PRO CYS GLU LYS VAL SER THR LEU PRO ALA ILE SEQRES 14 B 241 THR LEU LYS LEU GLY GLY LYS GLY TYR LYS LEU SER PRO SEQRES 15 B 241 GLU ASP TYR THR LEU LYS VAL SER GLN ALA GLY LYS THR SEQRES 16 B 241 LEU CYS LEU SER GLY PHE MET GLY MET ASP ILE PRO PRO SEQRES 17 B 241 PRO SER GLY PRO LEU TRP ILE LEU GLY ASP VAL PHE ILE SEQRES 18 B 241 GLY ARG TYR TYR THR VAL PHE ASP ARG ASP ASN ASN ARG SEQRES 19 B 241 VAL GLY PHE ALA GLU ALA ALA SEQRES 1 C 97 GLY PRO ILE PRO GLU VAL LEU LYS ASN TYR MET ASP ALA SEQRES 2 C 97 GLN TYR TYR GLY GLU ILE GLY ILE GLY THR PRO PRO GLN SEQRES 3 C 97 CYS PHE THR VAL VAL PHE ASP THR GLY SER SER ASN LEU SEQRES 4 C 97 TRP VAL PRO SER ILE HIS CYS LYS LEU LEU ASP ILE ALA SEQRES 5 C 97 CYS TRP ILE HIS HIS LYS TYR ASN SER ASP LYS SER SER SEQRES 6 C 97 THR TYR VAL LYS ASN GLY THR SER PHE ASP ILE HIS TYR SEQRES 7 C 97 GLY SER GLY SER LEU SER GLY TYR LEU SER GLN ASP THR SEQRES 8 C 97 VAL SER VAL PRO CYS GLN SEQRES 1 D 241 GLY GLY VAL LYS VAL GLU ARG GLN VAL PHE GLY GLU ALA SEQRES 2 D 241 THR LYS GLN PRO GLY ILE THR PHE ILE ALA ALA LYS PHE SEQRES 3 D 241 ASP GLY ILE LEU GLY MET ALA TYR PRO ARG ILE SER VAL SEQRES 4 D 241 ASN ASN VAL LEU PRO VAL PHE ASP ASN LEU MET GLN GLN SEQRES 5 D 241 LYS LEU VAL ASP GLN ASN ILE PHE SER PHE TYR LEU SER SEQRES 6 D 241 ARG ASP PRO ASP ALA GLN PRO GLY GLY GLU LEU MET LEU SEQRES 7 D 241 GLY GLY THR ASP SER LYS TYR TYR LYS GLY SER LEU SER SEQRES 8 D 241 TYR LEU ASN VAL THR ARG LYS ALA TYR TRP GLN VAL HIS SEQRES 9 D 241 LEU ASP GLN VAL GLU VAL ALA SER GLY LEU THR LEU CYS SEQRES 10 D 241 LYS GLU GLY CYS GLU ALA ILE VAL ASP THR GLY THR SER SEQRES 11 D 241 LEU MET VAL GLY PRO VAL ASP GLU VAL ARG GLU LEU GLN SEQRES 12 D 241 LYS ALA ILE GLY ALA VAL PRO LEU ILE GLN GLY GLU TYR SEQRES 13 D 241 MET ILE PRO CYS GLU LYS VAL SER THR LEU PRO ALA ILE SEQRES 14 D 241 THR LEU LYS LEU GLY GLY LYS GLY TYR LYS LEU SER PRO SEQRES 15 D 241 GLU ASP TYR THR LEU LYS VAL SER GLN ALA GLY LYS THR SEQRES 16 D 241 LEU CYS LEU SER GLY PHE MET GLY MET ASP ILE PRO PRO SEQRES 17 D 241 PRO SER GLY PRO LEU TRP ILE LEU GLY ASP VAL PHE ILE SEQRES 18 D 241 GLY ARG TYR TYR THR VAL PHE ASP ARG ASP ASN ASN ARG SEQRES 19 D 241 VAL GLY PHE ALA GLU ALA ALA MODRES 1LYA ASN A 70 ASN GLYCOSYLATION SITE MODRES 1LYA ASN B 199 ASN GLYCOSYLATION SITE MODRES 1LYA ASN C 70 ASN GLYCOSYLATION SITE MODRES 1LYA ASN D 199 ASN GLYCOSYLATION SITE HET NAG E 1 27 HET NAG E 2 27 HET BMA E 3 20 HET MAN E 4 22 HET NAG F 1 27 HET NAG F 2 27 HET BMA F 3 20 HET MAN F 4 22 HET NAG B 1 28 HET NAG D 1 28 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM MAN ALPHA-D-MANNOPYRANOSE FORMUL 5 NAG 6(C8 H15 N O6) FORMUL 5 BMA 2(C6 H12 O6) FORMUL 5 MAN 2(C6 H12 O6) FORMUL 9 HOH *46(H2 O) HELIX 1 A11 LYS A 47 ILE A 55 1 9 HELIX 2 A21 ILE B 124 ALA B 129 1 6 HELIX 3 A31 PRO B 149 LEU B 159 1 11 HELIX 4 A41 PRO B 240 GLY B 252 1 13 HELIX 5 A51 PRO B 264 LEU B 271 1 8 HELIX 6 A61 SER B 286 THR B 291 1 6 HELIX 7 A71 GLY B 322 GLY B 327 1 6 HELIX 8 A12 LYS C 47 ILE C 55 1 9 HELIX 9 A22 ILE D 124 ALA D 129 1 6 HELIX 10 A32 PRO D 149 LEU D 159 1 11 HELIX 11 A42 PRO D 240 GLY D 252 1 13 HELIX 12 A52 PRO D 264 LEU D 271 1 8 HELIX 13 A62 SER D 286 THR D 291 1 6 HELIX 14 A72 GLY D 322 GLY D 327 1 6 SHEET 1 I1 6 ILE A 3 LEU A 7 0 SHEET 2 I1 6 GLY B 178 GLY B 184 -1 SHEET 3 I1 6 ILE B 164 SER B 170 -1 SHEET 4 I1 6 TYR B 330 ASP B 334 -1 SHEET 5 I1 6 ASN B 337 ALA B 346 -1 SHEET 6 I1 6 TYR B 190 VAL B 200 -1 SHEET 1 II1 4 VAL B 254 LEU B 256 0 SHEET 2 II1 4 GLU B 260 ILE B 263 -1 SHEET 3 II1 4 LEU B 301 SER B 304 -1 SHEET 4 II1 4 GLN B 296 GLY B 298 -1 SHEET 1 1A1 9 VAL A 68 TYR A 78 0 SHEET 2 1A1 9 GLY A 81 ASP A 90 -1 SHEET 3 1A1 9 GLN B 113 LYS B 120 -1 SHEET 4 1A1 9 ASN A 38 SER A 43 1 SHEET 5 1A1 9 PHE B 131 MET B 137 -1 SHEET 6 1A1 9 GLN A 26 ASP A 33 1 SHEET 7 1A1 9 GLN A 14 GLY A 22 -1 SHEET 8 1A1 9 LYS A 8 TYR A 10 -1 SHEET 9 1A1 9 VAL B 110 ARG B 112 -1 SHEET 1 1B1 9 VAL A 68 TYR A 78 0 SHEET 2 1B1 9 GLY A 81 ASP A 90 -1 SHEET 3 1B1 9 GLN B 113 LYS B 120 -1 SHEET 4 1B1 9 ASN A 38 SER A 43 1 SHEET 5 1B1 9 PHE B 131 MET B 137 -1 SHEET 6 1B1 9 GLN A 26 ASP A 33 1 SHEET 7 1B1 9 GLN A 14 GLY A 22 -1 SHEET 8 1B1 9 THR A 91 CYS A 96 -1 SHEET 9 1B1 9 VAL B 110 ARG B 112 -1 SHEET 1 2A1 7 LYS B 281 LEU B 285 0 SHEET 2 2A1 7 ALA B 273 LEU B 278 -1 SHEET 3 2A1 7 TRP B 206 ALA B 216 -1 SHEET 4 2A1 7 LEU B 219 LEU B 221 -1 SHEET 5 2A1 7 LEU B 219 LYS B 223 1 SHEET 6 2A1 7 THR B 234 GLY B 239 -1 SHEET 7 2A1 7 GLY B 305 MET B 309 1 SHEET 1 2B1 7 LYS B 281 LEU B 285 0 SHEET 2 2B1 7 ALA B 273 LEU B 278 -1 SHEET 3 2B1 7 TRP B 206 ALA B 216 -1 SHEET 4 2B1 7 CYS B 226 ASP B 231 -1 SHEET 5 2B1 7 LEU B 219 LYS B 223 1 SHEET 6 2B1 7 THR B 234 GLY B 239 -1 SHEET 7 2B1 7 GLY B 305 MET B 309 1 SHEET 1 I2 6 ILE C 3 LEU C 7 0 SHEET 2 I2 6 GLY D 178 GLY D 184 -1 SHEET 3 I2 6 ILE D 164 SER D 170 -1 SHEET 4 I2 6 TYR D 330 ASP D 334 -1 SHEET 5 I2 6 ASN D 337 ALA D 346 -1 SHEET 6 I2 6 TYR D 190 VAL D 200 -1 SHEET 1 II2 4 VAL D 254 LEU D 256 0 SHEET 2 II2 4 GLU D 260 ILE D 263 -1 SHEET 3 II2 4 LEU D 301 SER D 304 -1 SHEET 4 II2 4 GLN D 296 GLY D 298 -1 SHEET 1 1A2 9 VAL C 68 TYR C 78 0 SHEET 2 1A2 9 GLY C 81 ASP C 90 -1 SHEET 3 1A2 9 GLN D 113 LYS D 120 -1 SHEET 4 1A2 9 ASN C 38 SER C 43 1 SHEET 5 1A2 9 PHE D 131 MET D 137 -1 SHEET 6 1A2 9 GLN C 26 ASP C 33 1 SHEET 7 1A2 9 GLN C 14 GLY C 22 -1 SHEET 8 1A2 9 LYS C 8 TYR C 10 -1 SHEET 9 1A2 9 VAL D 110 ARG D 112 -1 SHEET 1 1B2 9 VAL C 68 TYR C 78 0 SHEET 2 1B2 9 GLY C 81 ASP C 90 -1 SHEET 3 1B2 9 GLN D 113 LYS D 120 -1 SHEET 4 1B2 9 ASN C 38 SER C 43 1 SHEET 5 1B2 9 PHE D 131 MET D 137 -1 SHEET 6 1B2 9 GLN C 26 ASP C 33 1 SHEET 7 1B2 9 GLN C 14 GLY C 22 -1 SHEET 8 1B2 9 THR C 91 CYS C 96 -1 SHEET 9 1B2 9 VAL D 110 ARG D 112 -1 SHEET 1 2A2 7 LYS D 281 LEU D 285 0 SHEET 2 2A2 7 ALA D 273 LEU D 278 -1 SHEET 3 2A2 7 TRP D 206 ALA D 216 -1 SHEET 4 2A2 7 LEU D 219 LEU D 221 -1 SHEET 5 2A2 7 LEU D 219 LYS D 223 1 SHEET 6 2A2 7 THR D 234 GLY D 239 -1 SHEET 7 2A2 7 GLY D 305 MET D 309 1 SHEET 1 2B2 7 LYS D 281 LEU D 285 0 SHEET 2 2B2 7 ALA D 273 LEU D 278 -1 SHEET 3 2B2 7 TRP D 206 ALA D 216 -1 SHEET 4 2B2 7 CYS D 226 ASP D 231 -1 SHEET 5 2B2 7 LEU D 219 LYS D 223 1 SHEET 6 2B2 7 THR D 234 GLY D 239 -1 SHEET 7 2B2 7 GLY D 305 MET D 309 1 SSBOND 1 CYS A 27 CYS A 96 1555 1555 2.04 SSBOND 2 CYS A 46 CYS A 53 1555 1555 2.00 SSBOND 3 CYS B 222 CYS B 226 1555 1555 2.03 SSBOND 4 CYS B 265 CYS B 302 1555 1555 2.02 SSBOND 5 CYS C 27 CYS C 96 1555 1555 2.00 SSBOND 6 CYS C 46 CYS C 53 1555 1555 2.01 SSBOND 7 CYS D 222 CYS D 226 1555 1555 2.01 SSBOND 8 CYS D 265 CYS D 302 1555 1555 2.02 LINK ND2 ASN A 70 C1 NAG E 1 1555 1555 1.47 LINK C1 NAG B 1 ND2 ASN B 199 1555 1555 1.45 LINK ND2 ASN C 70 C1 NAG F 1 1555 1555 1.45 LINK C1 NAG D 1 ND2 ASN D 199 1555 1555 1.47 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 LINK O4 NAG E 2 C1 BMA E 3 1555 1555 1.41 LINK O6 BMA E 3 C1 MAN E 4 1555 1555 1.45 LINK O4 NAG F 1 C1 NAG F 2 1555 1555 1.44 LINK O4 NAG F 2 C1 BMA F 3 1555 1555 1.44 LINK O6 BMA F 3 C1 MAN F 4 1555 1555 1.45 CISPEP 1 THR A 23 PRO A 24 0 -9.43 CISPEP 2 VAL A 94 PRO A 95 0 -7.47 CISPEP 3 GLN B 176 PRO B 177 0 -0.07 CISPEP 4 PRO B 313 PRO B 314 0 8.20 CISPEP 5 GLY B 316 PRO B 317 0 -3.56 CISPEP 6 GLY C 1 PRO C 2 0 -11.58 CISPEP 7 THR C 23 PRO C 24 0 -11.78 CISPEP 8 VAL C 94 PRO C 95 0 -17.40 CISPEP 9 GLN D 176 PRO D 177 0 -5.50 CISPEP 10 GLY D 316 PRO D 317 0 2.06 CRYST1 125.900 125.900 104.100 90.00 90.00 120.00 P 65 12 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 0.007943 0.004586 0.000000 0.00000 SCALE2 0.000000 0.009172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009606 0.00000 MTRIX1 1 0.735300 0.674700 -0.064150 -9.57840 1 MTRIX2 1 0.608800 -0.699200 -0.374800 129.91299 1 MTRIX3 1 -0.297800 0.236600 -0.924900 10.65180 1