HEADER IMMUNE SYSTEM 20-MAY-15 5A2K TITLE CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD-TGALNAC-RP COMPND MOL_ID: 1; COMPND 2 MOLECULE: IG LAMBDA-1 CHAIN V REGION S43; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: RESIDUES 6-115,20-129; COMPND 5 SYNONYM: SCFV-SM3; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: ANTIGEN TN, THR IS COVALENTLY BOUND TO GALNAC; COMPND 9 CHAIN: P; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606 KEYWDS IMMUNE SYSTEM, GLYCOPEPTIDES, ANTIBODIES, MOLECULAR RECOGNITION, KEYWDS 2 CONFORMATION ANALYSIS, FUSION PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.MARTINEZ-SAEZ,J.CASTRO-LOPEZ,J.VALERO-GONZALEZ,D.MADARIAGA, AUTHOR 2 I.COMPANON,V.J.SOMOVILLA,M.SALVADO,J.L.ASENSIO,J.JIMENEZ-BARBERO, AUTHOR 3 A.AVENOZA,J.H.BUSTO,G.J.L.BERNARDES,J.M.PEREGRINA,R.HURTADO- AUTHOR 4 GUERRERO,F.CORZANA REVDAT 5 10-JAN-24 5A2K 1 HETSYN REVDAT 4 29-JUL-20 5A2K 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 26-AUG-15 5A2K 1 JRNL REVDAT 2 08-JUL-15 5A2K 1 JRNL REVDAT 1 03-JUN-15 5A2K 0 JRNL AUTH N.MARTINEZ-SAEZ,J.CASTRO-LOPEZ,J.VALERO-GONZALEZ, JRNL AUTH 2 D.MADARIAGA,I.COMPANON,V.J.SOMOVILLA,M.SALVADO,J.L.ASENSIO, JRNL AUTH 3 J.JIMENEZ-BARBERO,A.AVENOZA,J.H.BUSTO,G.J.L.BERNARDES, JRNL AUTH 4 J.M.PEREGRINA,R.HURTADO-GUERRERO,F.CORZANA JRNL TITL DECIPHERING THE NON-EQUIVALENCE OF SERINE AND THREONINE JRNL TITL 2 O-GLYCOSYLATION POINTS: IMPLICATIONS FOR MOLECULAR JRNL TITL 3 RECOGNITION OF THE TN ANTIGEN BY AN ANTI-MUC1 ANTIBODY. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 54 9830 2015 JRNL REFN ISSN 1433-7851 JRNL PMID 26118689 JRNL DOI 10.1002/ANIE.201502813 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 90.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 24300 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) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 736 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1734 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.94 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 61 REMARK 3 BIN FREE R VALUE : 0.2350 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1757 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.69000 REMARK 3 B22 (A**2) : 1.46000 REMARK 3 B33 (A**2) : -2.15000 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): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.693 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1833 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1692 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2467 ; 1.567 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3875 ; 0.813 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 6.982 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 76 ;34.297 ;23.947 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 274 ;13.786 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.376 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 279 ; 0.095 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2013 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 424 ; 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): 914 ; 1.482 ; 1.982 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 913 ; 1.482 ; 1.980 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 2.418 ; 2.951 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 919 ; 1.940 ; 2.312 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1 H 112 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9051 7.6649 21.0174 REMARK 3 T TENSOR REMARK 3 T11: 0.0073 T22: 0.0524 REMARK 3 T33: 0.0246 T12: 0.0028 REMARK 3 T13: 0.0009 T23: -0.0224 REMARK 3 L TENSOR REMARK 3 L11: 0.4395 L22: 0.7670 REMARK 3 L33: 1.3282 L12: 0.3924 REMARK 3 L13: -0.4091 L23: 0.1702 REMARK 3 S TENSOR REMARK 3 S11: 0.0325 S12: 0.0223 S13: 0.0423 REMARK 3 S21: 0.0323 S22: 0.0882 S23: -0.0473 REMARK 3 S31: -0.0265 S32: -0.0360 S33: -0.1207 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 1003 H 1107 REMARK 3 ORIGIN FOR THE GROUP (A): 10.5450 -5.4621 3.7481 REMARK 3 T TENSOR REMARK 3 T11: 0.0264 T22: 0.0336 REMARK 3 T33: 0.0123 T12: 0.0015 REMARK 3 T13: -0.0052 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 0.3600 L22: 0.7991 REMARK 3 L33: 0.4295 L12: -0.1376 REMARK 3 L13: -0.0550 L23: 0.2984 REMARK 3 S TENSOR REMARK 3 S11: 0.0189 S12: 0.0084 S13: -0.0467 REMARK 3 S21: 0.0158 S22: -0.0243 S23: -0.0022 REMARK 3 S31: -0.0827 S32: -0.0079 S33: 0.0055 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 ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 5A2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1290063822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25092 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.800 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 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: PDB ENTRY 1SM3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 17.70900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.20700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.39800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.20700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.70900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.39800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3270 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, P 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 ALA H 113 REMARK 465 SER H 114 REMARK 465 SER H 115 REMARK 465 GLY H 116 REMARK 465 GLY H 117 REMARK 465 GLY H 118 REMARK 465 GLY H 119 REMARK 465 SER H 120 REMARK 465 GLY H 121 REMARK 465 GLY H 122 REMARK 465 GLY H 123 REMARK 465 GLY H 124 REMARK 465 GLY H 125 REMARK 465 SER H 126 REMARK 465 SER H 127 REMARK 465 GLY H 128 REMARK 465 SER H 129 REMARK 465 SER H 130 REMARK 465 ASP H 1002 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 H 1 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 O HOH H 2015 O HOH H 2016 1.57 REMARK 500 O HOH H 2168 O HOH H 2170 1.62 REMARK 500 O HOH H 2005 O HOH H 2121 1.85 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 HOH H 2026 O HOH H 2163 2555 1.32 REMARK 500 O HOH H 2119 O HOH H 2159 4445 1.46 REMARK 500 O HOH H 2121 O HOH H 2156 4445 1.70 REMARK 500 O HOH H 2116 O HOH H 2123 4445 1.71 REMARK 500 O HOH H 2127 O HOH H 2155 4445 2.10 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 ARG H 52 C LEU H 52A N 0.213 REMARK 500 MET H 82 C ASN H 82A N 0.197 REMARK 500 ASN H 82A C ASN H 82B N 0.304 REMARK 500 ASN H 82B C LEU H 82C N 0.215 REMARK 500 THR H1027 C GLY H1027A N 0.258 REMARK 500 GLY H1027A C ALA H1027B N 0.252 REMARK 500 ALA H1027B C VAL H1027C N 0.172 REMARK 500 VAL H1106 C LEU H1106A N 0.204 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG H 52 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG H 52 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG H 66 NE - CZ - NH1 ANGL. DEV. = 5.4 DEGREES REMARK 500 ARG H 66 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG H 52 -157.16 -97.63 REMARK 500 VAL H 95 107.01 81.57 REMARK 500 ASP H1041 58.31 38.08 REMARK 500 THR H1051 -58.33 77.82 REMARK 500 ASN H1052 20.98 -141.46 REMARK 500 SER H1093 -45.19 64.72 REMARK 500 ASN H1094 13.53 -150.73 REMARK 500 PRO P 2 -157.44 -78.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASN H 82B -12.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5A2I RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD- SGALNAC-RP REMARK 900 RELATED ID: 5A2J RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH THE NAKED PEPTIDE REMARK 900 APDTRP REMARK 900 RELATED ID: 5A2L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD- CGALNAC-RP REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUE RANGE 1002-1107 FOR CHAIN H MAPS TO CHAIN L REMARK 999 OF PDB ENTRY 1SM3 REMARK 999 CHAIN P REPRESENTS A SHORTER VERISON OF THE PEPTIDE PRESENT REMARK 999 IN PDB ENTRY 1SM3 DBREF 5A2K H 6 113 UNP P01801 HV32_MOUSE 6 115 DBREF 5A2K H 1002 1107 UNP P01727 LV1E_MOUSE 20 129 DBREF 5A2K P 1 6 PDB 5A2K 5A2K 1 6 SEQADV 5A2K GLN H 1 UNP P01801 CLONING ARTIFACT SEQADV 5A2K VAL H 2 UNP P01801 CLONING ARTIFACT SEQADV 5A2K GLN H 3 UNP P01801 CLONING ARTIFACT SEQADV 5A2K LEU H 4 UNP P01801 CLONING ARTIFACT SEQADV 5A2K GLN H 5 UNP P01801 CLONING ARTIFACT SEQADV 5A2K GLY H 94 UNP P01801 INSERTION SEQADV 5A2K VAL H 95 UNP P01801 INSERTION SEQADV 5A2K GLY H 96 UNP P01801 INSERTION SEQADV 5A2K GLN H 97 UNP P01801 INSERTION SEQADV 5A2K H UNP P01801 THR 100 DELETION SEQADV 5A2K H UNP P01801 GLY 101 DELETION SEQADV 5A2K THR H 108 UNP P01801 LEU 110 CONFLICT SEQADV 5A2K SER H 114 UNP P01801 LINKER SEQADV 5A2K SER H 115 UNP P01801 LINKER SEQADV 5A2K GLY H 116 UNP P01801 LINKER SEQADV 5A2K GLY H 117 UNP P01801 LINKER SEQADV 5A2K GLY H 118 UNP P01801 LINKER SEQADV 5A2K GLY H 119 UNP P01801 LINKER SEQADV 5A2K SER H 120 UNP P01801 LINKER SEQADV 5A2K GLY H 121 UNP P01801 LINKER SEQADV 5A2K GLY H 122 UNP P01801 LINKER SEQADV 5A2K GLY H 123 UNP P01801 LINKER SEQADV 5A2K GLY H 124 UNP P01801 LINKER SEQADV 5A2K GLY H 125 UNP P01801 LINKER SEQADV 5A2K SER H 126 UNP P01801 LINKER SEQADV 5A2K SER H 127 UNP P01801 LINKER SEQADV 5A2K GLY H 128 UNP P01801 LINKER SEQADV 5A2K SER H 129 UNP P01801 LINKER SEQADV 5A2K SER H 130 UNP P01801 LINKER SEQADV 5A2K ASP H 1002 UNP P01727 GLN 20 CONFLICT SEQADV 5A2K ILE H 1003 UNP P01727 ALA 21 CONFLICT SEQADV 5A2K ALA H 1078 UNP P01727 THR 98 CONFLICT SEQADV 5A2K ILE H 1085 UNP P01727 MET 106 CONFLICT SEQRES 1 H 244 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 H 244 PRO GLY GLY SER MET LYS LEU SER CYS VAL ALA SER GLY SEQRES 3 H 244 PHE THR PHE SER ASN TYR TRP MET ASN TRP VAL ARG GLN SEQRES 4 H 244 SER PRO GLU LYS GLY LEU GLU TRP VAL ALA GLU ILE ARG SEQRES 5 H 244 LEU LYS SER ASN ASN TYR ALA THR HIS TYR ALA GLU SER SEQRES 6 H 244 VAL LYS GLY ARG PHE THR ILE SER ARG ASP ASP SER LYS SEQRES 7 H 244 SER SER VAL TYR LEU GLN MET ASN ASN LEU ARG ALA GLU SEQRES 8 H 244 ASP THR GLY ILE TYR TYR CYS THR GLY VAL GLY GLN PHE SEQRES 9 H 244 ALA TYR TRP GLY GLN GLY THR THR VAL THR VAL SER ALA SEQRES 10 H 244 SER SER GLY GLY GLY GLY SER GLY GLY GLY GLY GLY SER SEQRES 11 H 244 SER GLY SER SER ASP ILE VAL VAL THR GLN GLU SER ALA SEQRES 12 H 244 LEU THR THR SER PRO GLY GLU THR VAL THR LEU THR CYS SEQRES 13 H 244 ARG SER SER THR GLY ALA VAL THR THR SER ASN TYR ALA SEQRES 14 H 244 ASN TRP VAL GLN GLU LYS PRO ASP HIS LEU PHE THR GLY SEQRES 15 H 244 LEU ILE GLY GLY THR ASN ASN ARG ALA PRO GLY VAL PRO SEQRES 16 H 244 ALA ARG PHE SER GLY SER LEU ILE GLY ASP LYS ALA ALA SEQRES 17 H 244 LEU THR ILE THR GLY ALA GLN THR GLU ASP GLU ALA ILE SEQRES 18 H 244 TYR PHE CYS ALA LEU TRP TYR SER ASN HIS TRP VAL PHE SEQRES 19 H 244 GLY GLY GLY THR LYS LEU THR VAL LEU GLY SEQRES 1 P 6 ALA PRO ASP THR ARG PRO MODRES 5A2K THR P 4 THR GLYCOSYLATION SITE HET EDO H3001 4 HET EDO H3002 4 HET EDO H3004 4 HET EDO H3005 4 HET EDO H3006 4 HET EDO H3007 4 HET A2G P 10 14 HETNAM EDO 1,2-ETHANEDIOL HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN EDO ETHYLENE GLYCOL HETSYN A2G N-ACETYL-ALPHA-D-GALACTOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 A2G ALPHA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-D-GALACTOSE; 2- HETSYN 3 A2G ACETAMIDO-2-DEOXY-GALACTOSE; N-ACETYL-2-DEOXY-2-AMINO- HETSYN 4 A2G GALACTOSE FORMUL 3 EDO 6(C2 H6 O2) FORMUL 9 A2G C8 H15 N O6 FORMUL 10 HOH *188(H2 O) HELIX 1 1 THR H 28 TYR H 32 5 5 HELIX 2 2 LEU H 52A ASN H 54 5 5 HELIX 3 3 ASP H 73 LYS H 75 5 3 HELIX 4 4 ARG H 83 THR H 87 5 5 HELIX 5 5 THR H 1028 TYR H 1032 5 5 HELIX 6 6 GLN H 1079 GLU H 1083 5 5 SHEET 1 HA 4 GLN H 3 SER H 7 0 SHEET 2 HA 4 MET H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 HA 4 SER H 77 MET H 82 -1 O VAL H 78 N CYS H 22 SHEET 4 HA 4 PHE H 67 ASP H 72 -1 O THR H 68 N GLN H 81 SHEET 1 HB 4 GLY H 10 VAL H 12 0 SHEET 2 HB 4 THR H 107 VAL H 111 1 O THR H 108 N GLY H 10 SHEET 3 HB 4 GLY H 88 GLY H 94 -1 O GLY H 88 N VAL H 109 SHEET 4 HB 4 TYR H 102 TRP H 103 -1 O TYR H 102 N GLY H 94 SHEET 1 HC 6 GLY H 10 VAL H 12 0 SHEET 2 HC 6 THR H 107 VAL H 111 1 O THR H 108 N GLY H 10 SHEET 3 HC 6 GLY H 88 GLY H 94 -1 O GLY H 88 N VAL H 109 SHEET 4 HC 6 MET H 34 SER H 40 -1 O ASN H 35 N THR H 93 SHEET 5 HC 6 GLY H 44 ILE H 51 -1 O GLY H 44 N SER H 40 SHEET 6 HC 6 THR H 57 TYR H 59 -1 O HIS H 58 N GLU H 50 SHEET 1 HD 2 TYR H 102 TRP H 103 0 SHEET 2 HD 2 GLY H 88 GLY H 94 -1 O GLY H 94 N TYR H 102 SHEET 1 HE 4 VAL H1005 GLN H1007 0 SHEET 2 HE 4 THR H1018 SER H1025 -1 O ARG H1024 N THR H1006 SHEET 3 HE 4 LYS H1070 THR H1076 -1 O ALA H1071 N CYS H1023 SHEET 4 HE 4 PHE H1062 ILE H1067 -1 O SER H1063 N THR H1074 SHEET 1 HF 4 ALA H1010 THR H1013 0 SHEET 2 HF 4 THR H1102 VAL H1106 1 O LYS H1103 N LEU H1011 SHEET 3 HF 4 ALA H1084 TRP H1091 -1 O ALA H1084 N LEU H1104 SHEET 4 HF 4 TRP H1096 PHE H1098 -1 O VAL H1097 N LEU H1090 SHEET 1 HG 6 ALA H1010 THR H1013 0 SHEET 2 HG 6 THR H1102 VAL H1106 1 O LYS H1103 N LEU H1011 SHEET 3 HG 6 ALA H1084 TRP H1091 -1 O ALA H1084 N LEU H1104 SHEET 4 HG 6 ASN H1034 LYS H1039 -1 O ASN H1034 N ALA H1089 SHEET 5 HG 6 LEU H1043 GLY H1049 -1 O LEU H1043 N LYS H1039 SHEET 6 HG 6 ASN H1053 ARG H1054 -1 O ASN H1053 N GLY H1049 SHEET 1 HH 2 TRP H1096 PHE H1098 0 SHEET 2 HH 2 ALA H1084 TRP H1091 -1 O LEU H1090 N VAL H1097 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.04 SSBOND 2 CYS H 1023 CYS H 1088 1555 1555 2.07 LINK OG1 THR P 4 C1 A2G P 10 1555 1555 1.46 CISPEP 1 GLY H 96 GLN H 97 0 -6.50 CRYST1 35.418 68.796 90.414 90.00 90.00 90.00 P 21 21 21 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 0.028234 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014536 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011060 0.00000