HEADER IMMUNE SYSTEM 31-AUG-22 8AXH TITLE CRYSTAL STRUCTURE OF A MUC1-LIKE GLYCOPEPTIDE CONTAINING THE UNNATURAL TITLE 2 L-4-HYDROXYNORVALINE IN COMPLEX WITH SCFV-SM3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SINGLE-CHAIN VARIABLE ANTIBODY (SCFV) SM3; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MUCIN-1 SUBUNIT ALPHA; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: MUC1-NT,MUC1-ALPHA; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606 KEYWDS IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR I.BERMEJO,F.CORZANA,R.HURTADO-GUERRERO REVDAT 2 21-FEB-24 8AXH 1 JRNL REVDAT 1 09-AUG-23 8AXH 0 JRNL AUTH I.A.BERMEJO,A.GUERREIRO,A.EGUSKIZA,N.MARTINEZ-SAEZ, JRNL AUTH 2 F.S.LAZARIS,A.ASIN,V.J.SOMOVILLA,I.COMPANON,T.K.RAJU, JRNL AUTH 3 S.TADIC,P.GARRIDO,J.GARCIA-SANMARTIN,V.MANGINI,A.S.GROSSO, JRNL AUTH 4 F.MARCELO,A.AVENOZA,J.H.BUSTO,F.GARCIA-MARTIN, JRNL AUTH 5 R.HURTADO-GUERRERO,J.M.PEREGRINA,G.J.L.BERNARDES,A.MARTINEZ, JRNL AUTH 6 R.FIAMMENGO,F.CORZANA JRNL TITL STRUCTURE-GUIDED APPROACH FOR THE DEVELOPMENT OF JRNL TITL 2 MUC1-GLYCOPEPTIDE-BASED CANCER VACCINES WITH PREDICTABLE JRNL TITL 3 RESPONSES. JRNL REF JACS AU V. 4 150 2024 JRNL REFN ESSN 2691-3704 JRNL PMID 38274250 JRNL DOI 10.1021/JACSAU.3C00587 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 NUMBER OF REFLECTIONS : 17361 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) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 494 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1378 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 38 REMARK 3 BIN FREE R VALUE : 0.2380 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1773 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : 1.30000 REMARK 3 B33 (A**2) : -1.75000 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): 0.149 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.093 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.218 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1867 ; 0.009 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1646 ; 0.003 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2537 ; 1.546 ; 1.689 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3834 ; 0.702 ; 1.620 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 233 ; 8.732 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 8 ;25.385 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;14.539 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 284 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2106 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 386 ; 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): 917 ; 1.999 ; 2.243 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 916 ; 2.000 ; 2.243 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1143 ; 2.929 ; 3.346 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1144 ; 2.927 ; 3.346 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 950 ; 2.767 ; 2.607 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 951 ; 2.766 ; 2.607 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1391 ; 4.271 ; 3.760 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2048 ; 6.268 ;36.657 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2049 ; 6.267 ;36.671 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 8AXH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125307. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17900 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1SM3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350 DISODIUM HYDROGEN PHOSPHATE, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K 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 17.75050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.46150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.24500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.46150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.75050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.24500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: H, 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 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 SER H 984 REMARK 465 SER H 985 REMARK 465 SER H 986 REMARK 465 GLY H 987 REMARK 465 GLY H 988 REMARK 465 GLY H 989 REMARK 465 GLY H 990 REMARK 465 SER H 991 REMARK 465 GLY H 992 REMARK 465 GLY H 993 REMARK 465 GLY H 994 REMARK 465 GLY H 995 REMARK 465 GLY H 996 REMARK 465 SER H 997 REMARK 465 SER H 998 REMARK 465 GLY H 999 REMARK 465 SER H 1000 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 PRO H 41 O HOH H 1301 2.11 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 66 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG H 66 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 6 NE - CZ - NH2 ANGL. DEV. = 3.8 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 -157.06 -93.66 REMARK 500 VAL H 95 107.45 82.65 REMARK 500 ASP H1041 76.19 -7.49 REMARK 500 THR H1051 -56.05 76.66 REMARK 500 ASN H1052 20.96 -144.55 REMARK 500 SER H1093 -53.08 73.37 REMARK 500 ASN H1094 11.34 -151.94 REMARK 500 PRO A 2 -159.24 -80.58 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 H 1040 ASP H 1041 -115.13 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG H 52 0.24 SIDE CHAIN REMARK 500 ARG H 66 0.18 SIDE CHAIN 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 PRO H1040 -11.35 REMARK 500 REMARK 500 REMARK: NULL DBREF 8AXH H 1 1107 PDB 8AXH 8AXH 1 1107 DBREF 8AXH A 1 7 UNP P15941 MUC1_HUMAN 141 146 SEQADV 8AXH VAH A 4 UNP P15941 THR 144 ENGINEERED MUTATION SEQADV 8AXH NH2 A 8 UNP P15941 AMIDATION 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 SER 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 A 7 ALA PRO ASP VAH ARG PRO NH2 HET VAH A 4 8 HET NH2 A 8 1 HET EDO H1201 4 HET EDO H1202 4 HET EDO H1203 4 HET EDO H1204 4 HET EDO H1205 4 HET A2G A 101 14 HET EDO A 102 4 HETNAM VAH (3R)-3-HYDROXY-L-NORVALINE HETNAM NH2 AMINO GROUP HETNAM EDO 1,2-ETHANEDIOL HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETSYN VAH L-3-HYDROXYNORVALINE 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 2 VAH C5 H11 N O3 FORMUL 2 NH2 H2 N FORMUL 3 EDO 6(C2 H6 O2) FORMUL 8 A2G C8 H15 N O6 FORMUL 10 HOH *178(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 LEU H 52A ASN H 54 5 5 HELIX 3 AA3 ASP H 73 LYS H 75 5 3 HELIX 4 AA4 ARG H 83 THR H 87 5 5 HELIX 5 AA5 THR H 1028 TYR H 1032 5 5 HELIX 6 AA6 GLN H 1079 GLU H 1083 5 5 SHEET 1 AA1 4 GLN H 3 SER H 7 0 SHEET 2 AA1 4 MET H 18 SER H 25 -1 O SER H 21 N SER H 7 SHEET 3 AA1 4 SER H 77 MET H 82 -1 O MET H 82 N MET H 18 SHEET 4 AA1 4 PHE H 67 ASP H 72 -1 N SER H 70 O TYR H 79 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA2 6 GLY H 88 GLY H 94 -1 N TYR H 90 O THR H 107 SHEET 4 AA2 6 MET H 34 SER H 40 -1 N VAL H 37 O TYR H 91 SHEET 5 AA2 6 GLY H 44 ILE H 51 -1 O GLU H 46 N ARG H 38 SHEET 6 AA2 6 THR H 57 TYR H 59 -1 O HIS H 58 N GLU H 50 SHEET 1 AA3 4 GLY H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 107 VAL H 111 1 O THR H 110 N VAL H 12 SHEET 3 AA3 4 GLY H 88 GLY H 94 -1 N TYR H 90 O THR H 107 SHEET 4 AA3 4 TYR H 102 TRP H 103 -1 O TYR H 102 N GLY H 94 SHEET 1 AA4 4 VAL H1005 GLN H1007 0 SHEET 2 AA4 4 THR H1018 SER H1025 -1 O ARG H1024 N THR H1006 SHEET 3 AA4 4 LYS H1070 THR H1076 -1 O LEU H1073 N LEU H1021 SHEET 4 AA4 4 PHE H1062 ILE H1067 -1 N SER H1063 O THR H1074 SHEET 1 AA5 6 ALA H1010 THR H1013 0 SHEET 2 AA5 6 THR H1102 VAL H1106 1 O THR H1105 N THR H1013 SHEET 3 AA5 6 ALA H1084 TYR H1092 -1 N ALA H1084 O LEU H1104 SHEET 4 AA5 6 ASN H1034 LYS H1039 -1 N GLU H1038 O ILE H1085 SHEET 5 AA5 6 LEU H1043 GLY H1049 -1 O THR H1045 N GLN H1037 SHEET 6 AA5 6 ASN H1053 ARG H1054 -1 O ASN H1053 N GLY H1049 SHEET 1 AA6 4 ALA H1010 THR H1013 0 SHEET 2 AA6 4 THR H1102 VAL H1106 1 O THR H1105 N THR H1013 SHEET 3 AA6 4 ALA H1084 TYR H1092 -1 N ALA H1084 O LEU H1104 SHEET 4 AA6 4 HIS H1095 PHE H1098 -1 O HIS H1095 N TYR H1092 SSBOND 1 CYS H 22 CYS H 92 1555 1555 2.09 SSBOND 2 CYS H 1023 CYS H 1088 1555 1555 2.07 LINK C ASP A 3 N VAH A 4 1555 1555 1.35 LINK C VAH A 4 N ARG A 6 1555 1555 1.34 LINK OG1 VAH A 4 C1 A2G A 101 1555 1555 1.45 LINK C PRO A 7 N NH2 A 8 1555 1555 1.31 CISPEP 1 GLY H 96 GLN H 97 0 -11.92 CRYST1 35.501 68.490 90.923 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 0.028168 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014601 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010998 0.00000