PDB Short entry for 3WSR HEADER SUGAR BINDING PROTEIN 20-MAR-14 3WSR TITLE CRYSTAL STRUCTURE OF CLEC-2 IN COMPLEX WITH O-GLYCOSYLATED PODOPLANIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-TYPE LECTIN DOMAIN FAMILY 1 MEMBER B; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CLEC-2, UNP RESIDUES 96-221; COMPND 5 SYNONYM: C-TYPE LECTIN-LIKE RECEPTOR 2, CLEC-2; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: PEPTIDE FROM PODOPLANIN; COMPND 10 CHAIN: C, D; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CLEC1B, CLEC2, UNQ721/PRO1384; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA 2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606 KEYWDS C-TYPE LECTIN FOLD, CELL SURFACE RECEPTOR, PODOPLANIN, O- KEYWDS 2 GLYCOSYLATED, EXTRACELLULAR REGION, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.NAGAE,K.MORITA-MATSUMOTO,M.KATO,M.KATO-KANEKO,Y.KATO,Y.YAMAGUCHI REVDAT 5 08-NOV-23 3WSR 1 HETSYN REVDAT 4 29-JUL-20 3WSR 1 COMPND REMARK SEQADV HETNAM REVDAT 4 2 1 LINK SITE ATOM REVDAT 3 22-NOV-17 3WSR 1 REMARK REVDAT 2 24-DEC-14 3WSR 1 JRNL REVDAT 1 22-OCT-14 3WSR 0 JRNL AUTH M.NAGAE,K.MORITA-MATSUMOTO,M.KATO,M.KATO-KANEKO,Y.KATO, JRNL AUTH 2 Y.YAMAGUCHI JRNL TITL A PLATFORM OF C-TYPE LECTIN-LIKE RECEPTOR CLEC-2 FOR BINDING JRNL TITL 2 O-GLYCOSYLATED PODOPLANIN AND NONGLYCOSYLATED RHODOCYTIN JRNL REF STRUCTURE V. 22 1711 2014 JRNL REFN ISSN 0969-2126 JRNL PMID 25458834 JRNL DOI 10.1016/J.STR.2014.09.009 REMARK 2 REMARK 2 RESOLUTION. 1.91 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) : 1.91 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 20339 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1022 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.96 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1405 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2570 REMARK 3 BIN FREE R VALUE SET COUNT : 56 REMARK 3 BIN FREE R VALUE : 0.3530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2166 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 36 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.93000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.73000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.169 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.127 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.343 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.937 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): 2327 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2043 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3141 ; 1.368 ; 1.951 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4701 ; 0.825 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 257 ; 7.048 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;34.989 ;24.032 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 380 ;13.712 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;13.864 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 322 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2577 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 583 ; 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): 1040 ; 1.905 ; 2.672 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1039 ; 1.905 ; 2.672 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1293 ; 3.099 ; 3.989 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1294 ; 3.098 ; 3.989 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1287 ; 2.054 ; 2.872 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1287 ; 2.054 ; 2.872 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1849 ; 3.386 ; 4.202 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2598 ; 5.092 ;21.201 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2593 ; 5.095 ;21.206 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 3WSR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000096745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : SI(111) DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : MONOCHROMETER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21375 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.49500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.300 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 CODE 2C6U REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL (PH 8.5), 25% (W/V) REMARK 280 POLYETHYLENE GLYCOL (PEG) 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 25.59700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 1720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7440 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, F 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 A 94 REMARK 465 SER A 95 REMARK 465 GLY A 96 REMARK 465 HIS A 97 REMARK 465 LYS A 98 REMARK 465 SER A 99 REMARK 465 SER A 100 REMARK 465 GLY A 221 REMARK 465 GLY B 94 REMARK 465 SER B 95 REMARK 465 GLY B 96 REMARK 465 HIS B 97 REMARK 465 LYS B 98 REMARK 465 SER B 99 REMARK 465 SER B 100 REMARK 465 GLY B 221 REMARK 465 GLU C 38 REMARK 465 GLY C 39 REMARK 465 GLY C 40 REMARK 465 VAL C 41 REMARK 465 ALA C 42 REMARK 465 MET C 43 REMARK 465 PRO C 44 REMARK 465 GLY C 45 REMARK 465 GLU D 38 REMARK 465 GLY D 39 REMARK 465 GLY D 40 REMARK 465 VAL D 41 REMARK 465 ALA D 42 REMARK 465 MET D 43 REMARK 465 PRO D 44 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 A 315 O HOH A 316 2645 1.98 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 LEU B 214 CA - CB - CG ANGL. DEV. = 15.7 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 ASN A 192 18.62 57.90 REMARK 500 ASN B 105 -1.34 75.56 REMARK 500 ILE B 140 79.62 -100.20 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 ASP A 111 SER A 112 -147.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2C6U RELATED DB: PDB REMARK 900 LIGAND-FREE FORM DBREF 3WSR A 96 221 UNP Q9P126 CLC1B_HUMAN 96 221 DBREF 3WSR B 96 221 UNP Q9P126 CLC1B_HUMAN 96 221 DBREF 3WSR C 38 54 UNP Q86YL7 PDPN_HUMAN 38 54 DBREF 3WSR D 38 54 UNP Q86YL7 PDPN_HUMAN 38 54 SEQADV 3WSR GLY A 94 UNP Q9P126 EXPRESSION TAG SEQADV 3WSR SER A 95 UNP Q9P126 EXPRESSION TAG SEQADV 3WSR SER A 99 UNP Q9P126 CYS 99 ENGINEERED MUTATION SEQADV 3WSR GLY B 94 UNP Q9P126 EXPRESSION TAG SEQADV 3WSR SER B 95 UNP Q9P126 EXPRESSION TAG SEQADV 3WSR SER B 99 UNP Q9P126 CYS 99 ENGINEERED MUTATION SEQADV 3WSR CYS C 55 UNP Q86YL7 EXPRESSION TAG SEQADV 3WSR CYS D 55 UNP Q86YL7 EXPRESSION TAG SEQRES 1 A 128 GLY SER GLY HIS LYS SER SER PRO CYS ASP THR ASN TRP SEQRES 2 A 128 ARG TYR TYR GLY ASP SER CYS TYR GLY PHE PHE ARG HIS SEQRES 3 A 128 ASN LEU THR TRP GLU GLU SER LYS GLN TYR CYS THR ASP SEQRES 4 A 128 MET ASN ALA THR LEU LEU LYS ILE ASP ASN ARG ASN ILE SEQRES 5 A 128 VAL GLU TYR ILE LYS ALA ARG THR HIS LEU ILE ARG TRP SEQRES 6 A 128 VAL GLY LEU SER ARG GLN LYS SER ASN GLU VAL TRP LYS SEQRES 7 A 128 TRP GLU ASP GLY SER VAL ILE SER GLU ASN MET PHE GLU SEQRES 8 A 128 PHE LEU GLU ASP GLY LYS GLY ASN MET ASN CYS ALA TYR SEQRES 9 A 128 PHE HIS ASN GLY LYS MET HIS PRO THR PHE CYS GLU ASN SEQRES 10 A 128 LYS HIS TYR LEU MET CYS GLU ARG LYS ALA GLY SEQRES 1 B 128 GLY SER GLY HIS LYS SER SER PRO CYS ASP THR ASN TRP SEQRES 2 B 128 ARG TYR TYR GLY ASP SER CYS TYR GLY PHE PHE ARG HIS SEQRES 3 B 128 ASN LEU THR TRP GLU GLU SER LYS GLN TYR CYS THR ASP SEQRES 4 B 128 MET ASN ALA THR LEU LEU LYS ILE ASP ASN ARG ASN ILE SEQRES 5 B 128 VAL GLU TYR ILE LYS ALA ARG THR HIS LEU ILE ARG TRP SEQRES 6 B 128 VAL GLY LEU SER ARG GLN LYS SER ASN GLU VAL TRP LYS SEQRES 7 B 128 TRP GLU ASP GLY SER VAL ILE SER GLU ASN MET PHE GLU SEQRES 8 B 128 PHE LEU GLU ASP GLY LYS GLY ASN MET ASN CYS ALA TYR SEQRES 9 B 128 PHE HIS ASN GLY LYS MET HIS PRO THR PHE CYS GLU ASN SEQRES 10 B 128 LYS HIS TYR LEU MET CYS GLU ARG LYS ALA GLY SEQRES 1 C 18 GLU GLY GLY VAL ALA MET PRO GLY ALA GLU ASP ASP VAL SEQRES 2 C 18 VAL THR PRO GLY CYS SEQRES 1 D 18 GLU GLY GLY VAL ALA MET PRO GLY ALA GLU ASP ASP VAL SEQRES 2 D 18 VAL THR PRO GLY CYS MODRES 3WSR THR C 52 THR GLYCOSYLATION SITE MODRES 3WSR THR D 52 THR GLYCOSYLATION SITE HET A2G E 1 14 HET GAL E 2 11 HET SIA E 3 20 HET A2G F 1 14 HET GAL F 2 11 HET SIA F 3 20 HETNAM A2G 2-ACETAMIDO-2-DEOXY-ALPHA-D-GALACTOPYRANOSE HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM SIA N-ACETYL-ALPHA-NEURAMINIC ACID 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 HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN SIA N-ACETYLNEURAMINIC ACID; SIALIC ACID; ALPHA-SIALIC HETSYN 2 SIA ACID; O-SIALIC ACID FORMUL 5 A2G 2(C8 H15 N O6) FORMUL 5 GAL 2(C6 H12 O6) FORMUL 5 SIA 2(C11 H19 N O9) FORMUL 7 HOH *36(H2 O) HELIX 1 1 THR A 122 MET A 133 1 12 HELIX 2 2 ASN A 142 THR A 153 1 12 HELIX 3 3 SER A 179 LEU A 186 5 8 HELIX 4 4 THR B 122 MET B 133 1 12 HELIX 5 5 ASN B 142 THR B 153 1 12 HELIX 6 6 MET B 182 LEU B 186 5 5 SHEET 1 A 4 ARG A 107 TYR A 109 0 SHEET 2 A 4 SER A 112 LEU A 121 -1 O TYR A 114 N ARG A 107 SHEET 3 A 4 HIS A 212 LYS A 219 -1 O ARG A 218 N CYS A 113 SHEET 4 A 4 THR A 136 LEU A 137 -1 N THR A 136 O GLU A 217 SHEET 1 B 3 ARG A 157 SER A 162 0 SHEET 2 B 3 CYS A 195 HIS A 199 -1 O PHE A 198 N ARG A 157 SHEET 3 B 3 LYS A 202 THR A 206 -1 O LYS A 202 N HIS A 199 SHEET 1 C 4 ARG B 107 TYR B 109 0 SHEET 2 C 4 SER B 112 LEU B 121 -1 O TYR B 114 N ARG B 107 SHEET 3 C 4 HIS B 212 LYS B 219 -1 O ARG B 218 N CYS B 113 SHEET 4 C 4 THR B 136 LEU B 137 -1 N THR B 136 O GLU B 217 SHEET 1 D 3 ARG B 157 SER B 162 0 SHEET 2 D 3 CYS B 195 HIS B 199 -1 O PHE B 198 N ARG B 157 SHEET 3 D 3 LYS B 202 THR B 206 -1 O LYS B 202 N HIS B 199 SSBOND 1 CYS A 102 CYS A 113 1555 1555 2.02 SSBOND 2 CYS A 130 CYS A 216 1555 1555 2.06 SSBOND 3 CYS A 195 CYS A 208 1555 1555 2.04 SSBOND 4 CYS B 102 CYS B 113 1555 1555 2.05 SSBOND 5 CYS B 130 CYS B 216 1555 1555 2.03 SSBOND 6 CYS B 195 CYS B 208 1555 1555 2.04 SSBOND 7 CYS C 55 CYS D 55 1555 1555 2.00 LINK OG1 THR C 52 C1 A2G E 1 1555 1555 1.44 LINK OG1 THR D 52 C1 A2G F 1 1555 1555 1.46 LINK O3 A2G E 1 C1 GAL E 2 1555 1555 1.45 LINK O6 A2G E 1 C2 SIA E 3 1555 1555 1.43 LINK O3 A2G F 1 C1 GAL F 2 1555 1555 1.45 LINK O6 A2G F 1 C2 SIA F 3 1555 1555 1.43 CRYST1 54.369 51.194 54.099 90.00 112.77 90.00 P 1 21 1 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 0.018393 0.000000 0.007720 0.00000 SCALE2 0.000000 0.019534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020047 0.00000