HEADER DE NOVO PROTEIN 24-FEB-26 23WT TITLE DE NOVO DESIGN OF BINDER (#13136) TO MONOMERIC CU/ZN-SUPEROXIDE TITLE 2 DISMUTASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SOD1 BINDER #13136; COMPND 3 CHAIN: E, A, D, C, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SOD1, ARTIFICIAL PROTEIN, BINDER, ALS, DE NOVO PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.TAKAHASHI,N.MURAKI,Y.FURUKAWA REVDAT 1 30-SEP-26 23WT 0 JRNL AUTH M.TAKAHASHI,N.MURAKI,Y.FURUKAWA JRNL TITL DE NOVO DESIGNED BINDERS SUPPRESS AGGREGATION OF JRNL TITL 2 CU/ZN-SUPEROXIDE DISMUTASE IMPLICATED IN AMYOTROPHIC LATERAL JRNL TITL 3 SCLEROSIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22707 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1137 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1685 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE SET COUNT : 72 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3706 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 73.15 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 69.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.23000 REMARK 3 B22 (A**2) : 1.23000 REMARK 3 B33 (A**2) : -2.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.413 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.300 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.220 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.299 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.908 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3735 ; 0.008 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3633 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5021 ; 2.028 ; 1.877 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8526 ; 0.683 ; 1.821 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 478 ; 7.034 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 769 ;16.462 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 598 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4111 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 597 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1927 ; 6.411 ; 6.565 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1928 ; 6.409 ; 6.567 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2400 ; 9.340 ;11.808 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2401 ; 9.339 ;11.810 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1808 ; 9.801 ; 7.549 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1805 ; 9.793 ; 7.544 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2622 ;15.096 ;13.386 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3870 ;16.481 ;68.030 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3871 ;16.479 ;68.040 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 23WT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300070376. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-DEC-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL45XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23846 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.35200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M ZINC ACETATE, 10% (W/V) REMARK 280 POLYETHYLENE GLYCOL 8000, 0.1M MES PH 6.0, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 68.89950 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 34.44975 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.34925 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 5 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 70 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY E -1 REMARK 465 PRO E 0 REMARK 465 GLU E 1 REMARK 465 GLN E 2 REMARK 465 ILE E 3 REMARK 465 LYS E 95 REMARK 465 GLU E 96 REMARK 465 VAL E 97 REMARK 465 ALA E 98 REMARK 465 GLU E 99 REMARK 465 LYS E 100 REMARK 465 GLU A 99 REMARK 465 LYS A 100 REMARK 465 GLU D 96 REMARK 465 VAL D 97 REMARK 465 ALA D 98 REMARK 465 GLU D 99 REMARK 465 LYS D 100 REMARK 465 GLU C 96 REMARK 465 VAL C 97 REMARK 465 ALA C 98 REMARK 465 GLU C 99 REMARK 465 LYS C 100 REMARK 465 VAL B 97 REMARK 465 ALA B 98 REMARK 465 GLU B 99 REMARK 465 LYS B 100 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 GLU E 17 CG CD OE1 OE2 REMARK 470 LYS E 21 CG CD CE NZ REMARK 470 LYS E 28 CG CD CE NZ REMARK 470 GLU E 49 CG CD OE1 OE2 REMARK 470 LYS E 73 CG CD CE NZ REMARK 470 LYS E 89 CG CD CE NZ REMARK 470 GLU E 94 CG CD OE1 OE2 REMARK 470 GLU A 17 CG CD OE1 OE2 REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 470 LYS A 52 CG CD CE NZ REMARK 470 LYS A 58 CG CD CE NZ REMARK 470 LYS A 73 CG CD CE NZ REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 GLU A 77 CG CD OE1 OE2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 GLU A 84 CG CD OE1 OE2 REMARK 470 LYS A 95 CG CD CE NZ REMARK 470 GLU A 96 CG CD OE1 OE2 REMARK 470 VAL A 97 CG1 CG2 REMARK 470 GLU D 17 CG CD OE1 OE2 REMARK 470 LYS D 21 CG CD CE NZ REMARK 470 GLU D 69 CG CD OE1 OE2 REMARK 470 LYS D 87 CG CD CE NZ REMARK 470 LYS D 88 CG CD CE NZ REMARK 470 GLU D 91 CG CD OE1 OE2 REMARK 470 LYS D 95 CG CD CE NZ REMARK 470 GLU C 17 CG CD OE1 OE2 REMARK 470 GLU C 32 CG CD OE1 OE2 REMARK 470 LYS C 52 CG CD CE NZ REMARK 470 LYS C 58 CG CD CE NZ REMARK 470 LYS C 73 CG CD CE NZ REMARK 470 GLU C 77 CG CD OE1 OE2 REMARK 470 GLU C 81 CG CD OE1 OE2 REMARK 470 GLU C 84 CG CD OE1 OE2 REMARK 470 LYS C 88 CG CD CE NZ REMARK 470 GLU C 94 CG CD OE1 OE2 REMARK 470 LYS C 95 CG CD CE NZ REMARK 470 GLU B 17 CG CD OE1 OE2 REMARK 470 GLU B 48 CG CD OE1 OE2 REMARK 470 GLU B 49 CG CD OE1 OE2 REMARK 470 LYS B 88 CG CD CE NZ REMARK 470 GLU B 91 CG CD OE1 OE2 REMARK 470 LYS B 95 CG CD CE NZ REMARK 470 GLU B 96 CG CD OE1 OE2 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 OE2 GLU D 63 ZN ZN D 201 1.65 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 D 81 CD GLU D 81 OE1 0.066 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 GLU D 63 N - CA - CB ANGL. DEV. = -11.1 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 PRO D 0 56.47 -96.04 REMARK 500 GLU C 94 39.89 -67.22 REMARK 500 PRO B 0 59.01 -95.10 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 GLY D 13 LYS D 14 -139.52 REMARK 500 GLY B 13 LYS B 14 -138.43 REMARK 500 REMARK 500 REMARK: NULL 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 B 206 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU E 32 OE2 REMARK 620 2 HIS B 93 ND1 51.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN E 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 47 OD1 REMARK 620 2 HIS E 93 ND1 64.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 65 OD1 REMARK 620 2 GLU B 85 OE2 86.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A -1 N REMARK 620 2 LYS D 58 NZ 97.7 REMARK 620 3 GLU B 77 OE2 115.8 105.7 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 29 OD2 REMARK 620 2 HIS D 93 ND1 85.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 47 OD1 REMARK 620 2 ASP A 47 OD2 57.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY D -1 N REMARK 620 2 GLY D -1 O 77.4 REMARK 620 3 GLU D 1 OE1 110.5 82.7 REMARK 620 4 GLU B 70 OE2 129.9 83.2 112.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 204 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP D 47 OD1 REMARK 620 2 GLU D 94 OE2 68.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU D 70 OE2 REMARK 620 2 GLY B -1 N 130.1 REMARK 620 3 GLY B -1 O 96.3 78.3 REMARK 620 4 GLU B 1 OE1 112.2 117.6 100.8 REMARK 620 5 GLU B 63 OE1 93.8 75.9 152.8 98.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 203 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 32 OE1 REMARK 620 2 GLU B 32 OE2 53.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 47 OD1 REMARK 620 2 ASP C 47 OD2 51.0 REMARK 620 3 HIS C 93 ND1 112.1 65.5 REMARK 620 N 1 2 DBREF 23WT E -1 100 PDB 23WT 23WT -1 100 DBREF 23WT A -1 100 PDB 23WT 23WT -1 100 DBREF 23WT D -1 100 PDB 23WT 23WT -1 100 DBREF 23WT C -1 100 PDB 23WT 23WT -1 100 DBREF 23WT B -1 100 PDB 23WT 23WT -1 100 SEQRES 1 E 102 GLY PRO GLU GLN ILE ASN VAL THR VAL PRO ILE ASN ILE SEQRES 2 E 102 ASN GLY LYS SER VAL GLU ASP VAL ILE LYS ASN ALA LYS SEQRES 3 E 102 THR ILE ILE LYS ASP TYR GLN GLU ALA GLY VAL LYS VAL SEQRES 4 E 102 SER ILE GLU VAL ILE LYS GLU ALA TYR ASP GLU GLU THR SEQRES 5 E 102 GLY LYS LYS PHE LYS VAL SER LYS LYS ILE GLU ILE GLU SEQRES 6 E 102 PRO ASP ASP THR ASP GLU GLU ILE GLU LYS LYS LEU LYS SEQRES 7 E 102 GLU ALA ILE LYS GLU VAL GLU GLU GLU LEU LYS LYS LYS SEQRES 8 E 102 MET GLU GLU HIS GLU LYS GLU VAL ALA GLU LYS SEQRES 1 A 102 GLY PRO GLU GLN ILE ASN VAL THR VAL PRO ILE ASN ILE SEQRES 2 A 102 ASN GLY LYS SER VAL GLU ASP VAL ILE LYS ASN ALA LYS SEQRES 3 A 102 THR ILE ILE LYS ASP TYR GLN GLU ALA GLY VAL LYS VAL SEQRES 4 A 102 SER ILE GLU VAL ILE LYS GLU ALA TYR ASP GLU GLU THR SEQRES 5 A 102 GLY LYS LYS PHE LYS VAL SER LYS LYS ILE GLU ILE GLU SEQRES 6 A 102 PRO ASP ASP THR ASP GLU GLU ILE GLU LYS LYS LEU LYS SEQRES 7 A 102 GLU ALA ILE LYS GLU VAL GLU GLU GLU LEU LYS LYS LYS SEQRES 8 A 102 MET GLU GLU HIS GLU LYS GLU VAL ALA GLU LYS SEQRES 1 D 102 GLY PRO GLU GLN ILE ASN VAL THR VAL PRO ILE ASN ILE SEQRES 2 D 102 ASN GLY LYS SER VAL GLU ASP VAL ILE LYS ASN ALA LYS SEQRES 3 D 102 THR ILE ILE LYS ASP TYR GLN GLU ALA GLY VAL LYS VAL SEQRES 4 D 102 SER ILE GLU VAL ILE LYS GLU ALA TYR ASP GLU GLU THR SEQRES 5 D 102 GLY LYS LYS PHE LYS VAL SER LYS LYS ILE GLU ILE GLU SEQRES 6 D 102 PRO ASP ASP THR ASP GLU GLU ILE GLU LYS LYS LEU LYS SEQRES 7 D 102 GLU ALA ILE LYS GLU VAL GLU GLU GLU LEU LYS LYS LYS SEQRES 8 D 102 MET GLU GLU HIS GLU LYS GLU VAL ALA GLU LYS SEQRES 1 C 102 GLY PRO GLU GLN ILE ASN VAL THR VAL PRO ILE ASN ILE SEQRES 2 C 102 ASN GLY LYS SER VAL GLU ASP VAL ILE LYS ASN ALA LYS SEQRES 3 C 102 THR ILE ILE LYS ASP TYR GLN GLU ALA GLY VAL LYS VAL SEQRES 4 C 102 SER ILE GLU VAL ILE LYS GLU ALA TYR ASP GLU GLU THR SEQRES 5 C 102 GLY LYS LYS PHE LYS VAL SER LYS LYS ILE GLU ILE GLU SEQRES 6 C 102 PRO ASP ASP THR ASP GLU GLU ILE GLU LYS LYS LEU LYS SEQRES 7 C 102 GLU ALA ILE LYS GLU VAL GLU GLU GLU LEU LYS LYS LYS SEQRES 8 C 102 MET GLU GLU HIS GLU LYS GLU VAL ALA GLU LYS SEQRES 1 B 102 GLY PRO GLU GLN ILE ASN VAL THR VAL PRO ILE ASN ILE SEQRES 2 B 102 ASN GLY LYS SER VAL GLU ASP VAL ILE LYS ASN ALA LYS SEQRES 3 B 102 THR ILE ILE LYS ASP TYR GLN GLU ALA GLY VAL LYS VAL SEQRES 4 B 102 SER ILE GLU VAL ILE LYS GLU ALA TYR ASP GLU GLU THR SEQRES 5 B 102 GLY LYS LYS PHE LYS VAL SER LYS LYS ILE GLU ILE GLU SEQRES 6 B 102 PRO ASP ASP THR ASP GLU GLU ILE GLU LYS LYS LEU LYS SEQRES 7 B 102 GLU ALA ILE LYS GLU VAL GLU GLU GLU LEU LYS LYS LYS SEQRES 8 B 102 MET GLU GLU HIS GLU LYS GLU VAL ALA GLU LYS HET ZN E 201 1 HET ZN A 201 1 HET ZN A 202 1 HET ZN A 203 1 HET ZN D 201 1 HET ZN D 202 1 HET ZN D 203 1 HET ZN D 204 1 HET ZN C 201 1 HET ZN B 201 1 HET ZN B 202 1 HET ZN B 203 1 HET ZN B 204 1 HET ZN B 205 1 HET ZN B 206 1 HETNAM ZN ZINC ION FORMUL 6 ZN 15(ZN 2+) HELIX 1 AA1 SER E 15 ALA E 33 1 19 HELIX 2 AA2 THR E 67 GLU E 91 1 25 HELIX 3 AA3 SER A 15 GLU A 32 1 18 HELIX 4 AA4 THR A 67 ALA A 98 1 32 HELIX 5 AA5 SER D 15 GLN D 31 1 17 HELIX 6 AA6 THR D 67 GLU D 94 1 28 HELIX 7 AA7 SER C 15 ALA C 33 1 19 HELIX 8 AA8 THR C 67 GLU C 94 1 28 HELIX 9 AA9 SER B 15 GLN B 31 1 17 HELIX 10 AB1 THR B 67 LYS B 95 1 29 SHEET 1 AA1 6 VAL E 5 ASN E 10 0 SHEET 2 AA1 6 VAL E 37 TYR E 46 1 O SER E 38 N VAL E 5 SHEET 3 AA1 6 LYS E 53 ILE E 62 -1 O ILE E 62 N VAL E 37 SHEET 4 AA1 6 GLN C 2 ASN C 10 -1 O ASN C 4 N LYS E 55 SHEET 5 AA1 6 VAL C 35 TYR C 46 1 O SER C 38 N VAL C 5 SHEET 6 AA1 6 LYS C 53 ILE C 62 -1 O PHE C 54 N ALA C 45 SHEET 1 AA2 6 LYS A 53 ILE A 62 0 SHEET 2 AA2 6 LYS A 36 TYR A 46 -1 N ALA A 45 O PHE A 54 SHEET 3 AA2 6 GLU A 1 ASN A 10 1 N VAL A 5 O SER A 38 SHEET 4 AA2 6 LYS D 53 ILE D 62 -1 O LYS D 55 N ASN A 4 SHEET 5 AA2 6 VAL D 35 TYR D 46 -1 N VAL D 37 O ILE D 62 SHEET 6 AA2 6 ILE D 3 ASN D 10 1 N VAL D 5 O SER D 38 SHEET 1 AA3 3 ILE B 3 ASN B 10 0 SHEET 2 AA3 3 VAL B 35 TYR B 46 1 O ILE B 42 N ILE B 9 SHEET 3 AA3 3 LYS B 53 ILE B 62 -1 O ILE B 62 N VAL B 37 LINK OE2 GLU E 32 ZN ZN B 206 1555 4554 1.83 LINK OD1 ASP E 47 ZN ZN E 201 1555 1555 2.56 LINK OD1 ASP E 65 ZN ZN B 202 1555 4554 2.09 LINK ND1 HIS E 93 ZN ZN E 201 1555 1555 2.00 LINK N GLY A -1 ZN ZN A 203 1555 1555 2.39 LINK OD2 ASP A 29 ZN ZN A 202 1555 1555 2.19 LINK OD1 ASP A 47 ZN ZN A 201 1555 1555 2.28 LINK OD2 ASP A 47 ZN ZN A 201 1555 1555 2.41 LINK ZN ZN A 202 ND1 HIS D 93 1555 1555 2.39 LINK ZN ZN A 203 NZ LYS D 58 1555 1555 2.25 LINK ZN ZN A 203 OE2 GLU B 77 1555 1555 2.18 LINK N GLY D -1 ZN ZN D 201 1555 1555 2.15 LINK O GLY D -1 ZN ZN D 201 1555 1555 2.15 LINK OE1 GLU D 1 ZN ZN D 201 1555 1555 1.95 LINK OD1 ASP D 47 ZN ZN D 204 1555 1555 2.59 LINK OE2 GLU D 70 ZN ZN B 201 1555 1555 2.06 LINK OE2 GLU D 94 ZN ZN D 204 1555 1555 2.57 LINK ZN ZN D 201 OE2 GLU B 70 1555 1555 2.19 LINK ZN ZN D 203 OE1 GLU B 32 3555 1555 2.30 LINK ZN ZN D 203 OE2 GLU B 32 3555 1555 2.58 LINK OD1 ASP C 47 ZN ZN C 201 1555 1555 2.65 LINK OD2 ASP C 47 ZN ZN C 201 1555 1555 2.45 LINK ND1 HIS C 93 ZN ZN C 201 1555 1555 2.68 LINK N GLY B -1 ZN ZN B 201 1555 1555 2.18 LINK O GLY B -1 ZN ZN B 201 1555 1555 2.04 LINK OE1 GLU B 1 ZN ZN B 201 1555 1555 1.87 LINK OE1 GLU B 63 ZN ZN B 201 1555 1555 2.22 LINK OE2 GLU B 83 ZN ZN B 205 1555 1555 1.95 LINK OE2 GLU B 85 ZN ZN B 202 1555 1555 2.38 LINK ND1 HIS B 93 ZN ZN B 206 1555 1555 1.96 CRYST1 93.710 93.710 137.799 90.00 90.00 90.00 P 41 20 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 0.010671 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010671 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007257 0.00000 CONECT 327 3712 CONECT 698 3712 CONECT 708 3715 CONECT 933 3714 CONECT 1071 3713 CONECT 1072 3713 CONECT 1460 3716 CONECT 1463 3716 CONECT 1478 3716 CONECT 1827 3719 CONECT 1917 3715 CONECT 2012 3721 CONECT 2194 3714 CONECT 2206 3719 CONECT 2580 3720 CONECT 2581 3720 CONECT 2935 3720 CONECT 2950 3721 CONECT 2953 3721 CONECT 2968 3721 CONECT 3445 3721 CONECT 3502 3716 CONECT 3563 3715 CONECT 3610 3725 CONECT 3628 3722 CONECT 3688 3726 CONECT 3712 327 698 CONECT 3713 1071 1072 CONECT 3714 933 2194 CONECT 3715 708 1917 3563 CONECT 3716 1460 1463 1478 3502 CONECT 3719 1827 2206 CONECT 3720 2580 2581 2935 CONECT 3721 2012 2950 2953 2968 CONECT 3721 3445 CONECT 3722 3628 CONECT 3725 3610 CONECT 3726 3688 MASTER 542 0 15 10 15 0 0 6 3721 5 38 40 END