HEADER ANTITUMOR PROTEIN 15-NOV-19 6TGG TITLE SCFV-1SM3 IN COMPLEX WITH GLYCOPEPTIDE CONTAINING AN SP2-IMINO SUGAR COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCFV_SM3; COMPND 3 CHAIN: H; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: MUCIN-1; COMPND 7 CHAIN: P; COMPND 8 SYNONYM: MUC-1,BREAST CARCINOMA-ASSOCIATED ANTIGEN DF3,CANCER ANTIGEN COMPND 9 15-3,CA 15-3,CARCINOMA-ASSOCIATED MUCIN,EPISIALIN,H23AG,KREBS VON DEN COMPND 10 LUNGEN-6,KL-6,PEMT,PEANUT-REACTIVE URINARY MUCIN,PUM,POLYMORPHIC COMPND 11 EPITHELIAL MUCIN,PEM,TUMOR-ASSOCIATED EPITHELIAL MEMBRANE ANTIGEN, COMPND 12 EMA,TUMOR-ASSOCIATED MUCIN; COMPND 13 ENGINEERED: YES; COMPND 14 OTHER_DETAILS: NOTE THAT THIS IS A MODIFIED GLYCOPEPTIDE CONTAINING COMPND 15 AN SP2-IMINO SUGAR. IN ADDITION, THE THR RESIDUE IS COVALENTLY BOUND COMPND 16 TO THE SP2-IMINO SUGAR (IT IS FOUND IN THE PDB AS A2G). 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 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606 KEYWDS ANTIBODY, SCFV, ANTIGEN TN, IMINOSUGAR, ANTI CANCER VACCINE, KEYWDS 2 CONFORMATIONAL ANALYSIS, ANTITUMOR PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.A.BERMEJO,C.D.NAVO,J.CASTRO-LOPEZ,E.M.SAMCHEZ-FERNANDEZ, AUTHOR 2 A.GUERREIRO,A.AVENOZA,J.H.BUSTO,F.GARCIA-MARTIN,S.I.NISHIMURA, AUTHOR 3 J.M.GARCIA-FERNANDEZ,C.ORTIZ-MELLET,G.J.L.BERNARDES,R.HURTADO- AUTHOR 4 GUERRERO,J.M.PEREGRINA,F.CORZANA REVDAT 3 24-JAN-24 6TGG 1 REMARK REVDAT 2 07-JUL-21 6TGG 1 JRNL REVDAT 1 08-APR-20 6TGG 0 JRNL AUTH I.A.BERMEJO,C.D.NAVO,J.CASTRO-LOPEZ,A.GUERREIRO, JRNL AUTH 2 E.JIMENEZ-MORENO,E.M.SANCHEZ FERNANDEZ,F.GARCIA-MARTIN, JRNL AUTH 3 H.HINOU,S.I.NISHIMURA,J.M.GARCIA FERNANDEZ,C.O.MELLET, JRNL AUTH 4 A.AVENOZA,J.H.BUSTO,G.J.L.BERNARDES,R.HURTADO-GUERRERO, JRNL AUTH 5 J.M.PEREGRINA,F.CORZANA JRNL TITL SYNTHESIS, CONFORMATIONAL ANALYSIS AND IN VIVO ASSAYS OF AN JRNL TITL 2 ANTI-CANCER VACCINE THAT FEATURES AN UNNATURAL ANTIGEN BASED JRNL TITL 3 ON AN SP 2 -IMINOSUGAR FRAGMENT. JRNL REF CHEM SCI V. 11 3996 2020 JRNL REFN ISSN 2041-6520 JRNL PMID 34122869 JRNL DOI 10.1039/C9SC06334J REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.21 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15042 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) : 0.175 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.800 REMARK 3 FREE R VALUE TEST SET COUNT : 441 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1095 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.73 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 32 REMARK 3 BIN FREE R VALUE : 0.2540 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 : 32 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.07000 REMARK 3 B22 (A**2) : 2.15000 REMARK 3 B33 (A**2) : -2.23000 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): 0.186 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.174 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.111 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.993 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.954 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1847 ; 0.012 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 1600 ; 0.002 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2506 ; 1.528 ; 1.671 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3739 ; 1.025 ; 1.673 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 232 ; 7.465 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 86 ;34.165 ;22.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 275 ;16.150 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;15.601 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 245 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2076 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 360 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : NULL 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6TGG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105431. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15528 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.800 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: 5OWP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 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 17.63550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.19650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.34450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.19650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.63550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.34450 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: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 7.0 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 SER H 990 REMARK 465 SER H 991 REMARK 465 SER 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 GLY H 998 REMARK 465 GLY H 999 REMARK 465 GLY H 1000 REMARK 465 GLY H 1001 REMARK 465 GLY H 1002 REMARK 465 SER H 1003 REMARK 465 SER H 1004 REMARK 465 GLY H 1005 REMARK 465 SER H 1006 REMARK 465 SER H 1007 REMARK 465 ASP H 1008 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 OG1 THR P 4 N1 N8W P 101 2.15 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 LYS H 43 -17.21 78.61 REMARK 500 ARG H 52 -153.04 -86.25 REMARK 500 VAL H 101 105.64 82.23 REMARK 500 THR H1060 -53.36 77.35 REMARK 500 ASN H1061 19.54 -144.02 REMARK 500 SER H1102 -52.95 76.95 REMARK 500 ASN H1103 17.50 -150.69 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 0.28 SIDE CHAIN REMARK 500 ARG H1063 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 1201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 1202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 1203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO H 1204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue N8W P 101 DBREF 6TGG H 1 1117 PDB 6TGG 6TGG 1 1117 DBREF 6TGG P 1 6 UNP P15941 MUC1_HUMAN 141 146 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 P 6 ALA PRO ASP THR ARG PRO HET EDO H1201 4 HET EDO H1202 4 HET EDO H1203 4 HET EDO H1204 4 HET N8W P 101 16 HETNAM EDO 1,2-ETHANEDIOL HETNAM N8W ~{N}-[(6~{S},7~{R},8~{S},8~{A}~{R})-7,8-BIS(OXIDANYL)- HETNAM 2 N8W 3-OXIDANYLIDENE-1,5,6,7,8,8~{A}-HEXAHYDRO-[1, HETNAM 3 N8W 3]OXAZOLO[3,4-A]PYRIDIN-6-YL]ETHANAMIDE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 N8W C9 H14 N2 O5 FORMUL 8 HOH *167(H2 O) HELIX 1 AA1 THR H 28 TYR H 32 5 5 HELIX 2 AA2 LEU H 53 ASN H 57 5 5 HELIX 3 AA3 ASP H 76 LYS H 78 5 3 HELIX 4 AA4 ARG H 89 THR H 93 5 5 HELIX 5 AA5 THR H 1037 TYR H 1041 5 5 HELIX 6 AA6 GLN H 1088 GLU H 1092 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 25 N GLN H 3 SHEET 3 AA1 4 SER H 80 MET H 85 -1 O LEU H 83 N LEU H 20 SHEET 4 AA1 4 PHE H 70 ASP H 75 -1 N SER H 73 O TYR H 82 SHEET 1 AA2 6 GLY H 10 VAL H 12 0 SHEET 2 AA2 6 THR H 113 VAL H 117 1 O THR H 116 N GLY H 10 SHEET 3 AA2 6 GLY H 94 GLY H 100 -1 N GLY H 94 O VAL H 115 SHEET 4 AA2 6 MET H 34 GLN H 39 -1 N VAL H 37 O TYR H 97 SHEET 5 AA2 6 LEU H 45 ILE H 51 -1 O ILE H 51 N MET H 34 SHEET 6 AA2 6 THR H 60 TYR H 62 -1 O HIS H 61 N GLU H 50 SHEET 1 AA3 4 GLY H 10 VAL H 12 0 SHEET 2 AA3 4 THR H 113 VAL H 117 1 O THR H 116 N GLY H 10 SHEET 3 AA3 4 GLY H 94 GLY H 100 -1 N GLY H 94 O VAL H 115 SHEET 4 AA3 4 TYR H 108 TRP H 109 -1 O TYR H 108 N GLY H 100 SHEET 1 AA4 4 VAL H1011 GLN H1013 0 SHEET 2 AA4 4 THR H1024 SER H1031 -1 O ARG H1030 N THR H1012 SHEET 3 AA4 4 LYS H1079 THR H1085 -1 O LEU H1082 N LEU H1027 SHEET 4 AA4 4 PHE H1071 ILE H1076 -1 N SER H1074 O ALA H1081 SHEET 1 AA5 6 ALA H1016 THR H1019 0 SHEET 2 AA5 6 THR H1111 VAL H1115 1 O THR H1114 N THR H1019 SHEET 3 AA5 6 ALA H1093 TRP H1100 -1 N ALA H1093 O LEU H1113 SHEET 4 AA5 6 ASN H1043 LYS H1048 -1 N GLU H1047 O ILE H1094 SHEET 5 AA5 6 LEU H1052 GLY H1058 -1 O LEU H1052 N LYS H1048 SHEET 6 AA5 6 ASN H1062 ARG H1063 -1 O ASN H1062 N GLY H1058 SHEET 1 AA6 4 ALA H1016 THR H1019 0 SHEET 2 AA6 4 THR H1111 VAL H1115 1 O THR H1114 N THR H1019 SHEET 3 AA6 4 ALA H1093 TRP H1100 -1 N ALA H1093 O LEU H1113 SHEET 4 AA6 4 TRP H1105 PHE H1107 -1 O VAL H1106 N LEU H1099 SSBOND 1 CYS H 22 CYS H 98 1555 1555 2.07 SSBOND 2 CYS H 1029 CYS H 1097 1555 1555 2.08 LINK OG1 THR P 4 C1 N8W P 101 1555 1555 1.38 CISPEP 1 GLY H 102 GLN H 103 0 -13.00 CISPEP 2 PRO H 1049 ASP H 1050 0 1.68 SITE 1 AC1 5 SER H 30 ASN H 31 LEU H 53 LYS H 54 SITE 2 AC1 5 SER H 55 SITE 1 AC2 5 GLN H1046 LYS H1048 PRO H1068 PHE H1071 SITE 2 AC2 5 HOH H1338 SITE 1 AC3 8 THR H1019 SER H1020 GLU H1023 PRO H1068 SITE 2 AC3 8 ALA H1069 HOH H1307 HOH H1358 HOH H1424 SITE 1 AC4 6 VAL H1025 THR H1026 GLN H1088 HOH H1302 SITE 2 AC4 6 HOH H1385 HOH H1407 SITE 1 AC5 7 TRP H 33 ASP P 3 THR P 4 ARG P 5 SITE 2 AC5 7 PRO P 6 HOH P 201 HOH P 202 CRYST1 35.271 68.689 90.393 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 0.028352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014558 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011063 0.00000