HEADER IMMUNE SYSTEM 20-MAY-15 5A2L TITLE CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD-CGALNAC-RP COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCFV-SM3; COMPND 3 CHAIN: H; COMPND 4 FRAGMENT: RESIDUES 6-115,20-129; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: MODIFIED ANTIGEN TN; COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES; COMPND 10 OTHER_DETAILS: CYS IS COVALENTLY BOUND TO GALNAC 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_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPICZALPHAA; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606 KEYWDS IMMUNE SYSTEM, PEPTIDE BINDING PROTEIN, GLYCOPEPTIDES, ANTIBODIES, KEYWDS 2 MOLECULAR RECOGNITION, 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 5A2L 1 HETSYN REVDAT 4 29-JUL-20 5A2L 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 26-AUG-15 5A2L 1 JRNL REVDAT 2 08-JUL-15 5A2L 1 JRNL REVDAT 1 03-JUN-15 5A2L 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. 1.79 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 19308 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.900 REMARK 3 FREE R VALUE TEST SET COUNT : 575 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1425 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.86 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 52 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1759 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 30 REMARK 3 SOLVENT ATOMS : 113 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.42000 REMARK 3 B22 (A**2) : -1.66000 REMARK 3 B33 (A**2) : 0.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.33000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.135 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.104 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.496 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1826 ; 0.011 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 1677 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2461 ; 1.528 ; 1.940 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3843 ; 0.767 ; 3.001 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 221 ; 6.715 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;32.849 ;24.026 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;14.683 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;19.595 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 278 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2019 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 425 ; 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 ; 1.920 ; 2.547 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 913 ; 1.918 ; 2.545 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1119 ; 3.199 ; 3.797 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 912 ; 2.286 ; 2.847 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 : 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 ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 5A2L 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_1290063827. 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 : I02 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 : 19905 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 64.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.980 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.60000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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 (%): 36.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 17.59500 REMARK 290 SMTRY3 2 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: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 1070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.1 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 GLN H 1 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 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 NH2 ARG H 66 OD2 ASP H 86 2.09 REMARK 500 OE1 GLN H 1079 O HOH H 2102 2.10 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 2064 O HOH H 2102 2645 1.28 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 0.281 REMARK 500 LEU H 52A C LYS H 52B N 0.232 REMARK 500 ASN H 82A C ASN H 82B N 0.313 REMARK 500 ASN H 82B C LEU H 82C N 0.219 REMARK 500 PHE H 98 C ALA H 101 N 0.196 REMARK 500 THR H1027 C GLY H1027A N 0.146 REMARK 500 GLY H1027A C ALA H1027B N 0.186 REMARK 500 ALA H1027B C VAL H1027C N 0.172 REMARK 500 VAL H1106 C LEU H1106A N 0.220 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. = 4.2 DEGREES REMARK 500 ARG H 66 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG H 66 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 THR H1027 O - C - N ANGL. DEV. = -12.3 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 VAL H 95 107.06 77.60 REMARK 500 PRO H1040 120.06 -27.31 REMARK 500 ASP H1041 69.61 64.07 REMARK 500 THR H1051 -54.08 79.34 REMARK 500 SER H1093 -60.18 74.51 REMARK 500 ASN H1094 19.00 -146.66 REMARK 500 PRO P 2 -157.92 -84.74 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 82A 12.45 REMARK 500 ASN H 82B 16.27 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: 5A2K RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SCFV-SM3 IN COMPLEX WITH APD- TGALNAC-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 5A2L H 6 113 UNP P01801 HVM32_MOUSE 6 115 DBREF 5A2L H 1003 1107 UNP P01727 LV1E_MOUSE 20 129 DBREF 5A2L P 1 6 PDB 5A2L 5A2L 1 6 SEQADV 5A2L GLN H 1 UNP P01801 CLONING ARTIFACT SEQADV 5A2L VAL H 2 UNP P01801 CLONING ARTIFACT SEQADV 5A2L GLN H 3 UNP P01801 CLONING ARTIFACT SEQADV 5A2L LEU H 4 UNP P01801 CLONING ARTIFACT SEQADV 5A2L GLN H 5 UNP P01801 CLONING ARTIFACT SEQADV 5A2L GLY H 94 UNP P01801 INSERTION SEQADV 5A2L VAL H 95 UNP P01801 THR 100 CONFLICT SEQADV 5A2L GLN H 97 UNP P01801 INSERTION SEQADV 5A2L THR H 108 UNP P01801 LEU 110 CONFLICT SEQADV 5A2L SER H 114 UNP P01801 LINKER SEQADV 5A2L SER H 115 UNP P01801 LINKER SEQADV 5A2L GLY H 116 UNP P01801 LINKER SEQADV 5A2L GLY H 117 UNP P01801 LINKER SEQADV 5A2L GLY H 118 UNP P01801 LINKER SEQADV 5A2L GLY H 119 UNP P01801 LINKER SEQADV 5A2L SER H 120 UNP P01801 LINKER SEQADV 5A2L GLY H 121 UNP P01801 LINKER SEQADV 5A2L GLY H 122 UNP P01801 LINKER SEQADV 5A2L GLY H 123 UNP P01801 LINKER SEQADV 5A2L GLY H 124 UNP P01801 LINKER SEQADV 5A2L GLY H 125 UNP P01801 LINKER SEQADV 5A2L SER H 126 UNP P01801 LINKER SEQADV 5A2L SER H 127 UNP P01801 LINKER SEQADV 5A2L GLY H 128 UNP P01801 LINKER SEQADV 5A2L SER H 129 UNP P01801 LINKER SEQADV 5A2L SER H 130 UNP P01801 LINKER SEQADV 5A2L ASP H 1002 UNP P01727 GLN 20 CONFLICT SEQADV 5A2L ILE H 1003 UNP P01727 ALA 21 CONFLICT SEQADV 5A2L ALA H 1078 UNP P01727 THR 98 CONFLICT SEQADV 5A2L 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 CYS ARG PRO HET EDO H3001 4 HET EDO H3002 4 HET EDO H3003 4 HET EDO H3004 4 HET A2G P1009 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 4(C2 H6 O2) FORMUL 7 A2G C8 H15 N O6 FORMUL 8 HOH *113(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 GLU H 61 LYS H 64 5 4 HELIX 4 4 ASP H 73 LYS H 75 5 3 HELIX 5 5 ARG H 83 THR H 87 5 5 HELIX 6 6 THR H 1028 TYR H 1032 5 5 HELIX 7 7 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 2.07 SSBOND 2 CYS H 1023 CYS H 1088 1555 1555 2.07 LINK SG CYS P 4 C1 A2G P1009 1555 1555 1.64 CISPEP 1 GLY H 96 GLN H 97 0 -2.93 CRYST1 46.080 35.190 66.290 90.00 103.01 90.00 P 1 21 1 2 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 0.021701 0.000000 0.005014 0.00000 SCALE2 0.000000 0.028417 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015483 0.00000