HEADER PROTEIN BINDING 02-JAN-25 9LAD TITLE CRYSTAL STRUCTURE OF THE COMPLEX BETWEEN NEURONAL PENTRAXIN 2 (NP2 TITLE 2 PTX) AND ANTIBODY FRAGMENT VHH N1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: N1 VHH; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEURONAL PENTRAXIN-2; COMPND 7 CHAIN: C; COMPND 8 SYNONYM: NP2,NEURONAL ACTIVITY-REGULATED PENTRAXIN,NEURONAL PENTRAXIN COMPND 9 II,NP-II; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 3 ORGANISM_TAXID: 30538; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: NPTX2, NARP; SOURCE 11 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 13 EXPRESSION_SYSTEM_CELL_LINE: EXPI293 KEYWDS NEURONAL PENTRAXIN, ESPS, SYNAPTIC ORGANIZER, AMPAR, NANOBODY, MASS KEYWDS 2 PHOTOMETRY, CHRONIC ITCH, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR J.M.M.CAAVEIRO,T.YOKOO,K.TSUMOTO REVDAT 2 07-JAN-26 9LAD 1 JRNL REVDAT 1 10-DEC-25 9LAD 0 JRNL AUTH T.YOKOO,M.NAKAKIDO,K.MATSUDA,J.M.M.CAAVEIRO, JRNL AUTH 2 J.FERNANDEZ-PEREZ,M.YUZAKI,K.TSUMOTO JRNL TITL DEVELOPMENT OF A VHH THAT INHIBITS THE BINDING OF NEURONAL JRNL TITL 2 PENTRAXIN 2 TO A POSTSYNAPTIC GLUTAMATE RECEPTOR, AMPAR. JRNL REF J.BIOL.CHEM. V. 302 10975 2025 JRNL REFN ESSN 1083-351X JRNL PMID 41308985 JRNL DOI 10.1016/J.JBC.2025.110975 REMARK 2 REMARK 2 RESOLUTION. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0425 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) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 28961 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.931 REMARK 3 FREE R VALUE TEST SET COUNT : 1428 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) : 2.02 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.07 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1626 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.3450 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.3510 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2542 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 125 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.38400 REMARK 3 B22 (A**2) : 1.78500 REMARK 3 B33 (A**2) : -3.16900 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): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.142 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.475 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 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): 2638 ; 0.007 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 2440 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3588 ; 1.618 ; 1.795 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5611 ; 0.548 ; 1.746 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 330 ; 7.802 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 14 ;10.082 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 420 ;13.330 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 384 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3200 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 638 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 477 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 42 ; 0.169 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1276 ; 0.185 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 134 ; 0.243 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.137 ; 0.200 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): 2 ; 0.230 ; 0.200 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): 1314 ; 2.531 ; 3.150 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1314 ; 2.526 ; 3.149 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1643 ; 3.568 ; 5.651 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1644 ; 3.568 ; 5.652 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1324 ; 3.270 ; 3.415 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1325 ; 3.269 ; 3.417 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1944 ; 4.797 ; 6.135 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1945 ; 4.796 ; 6.137 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 : B 1 B 121 REMARK 3 ORIGIN FOR THE GROUP (A): 22.2379 10.1837 8.6533 REMARK 3 T TENSOR REMARK 3 T11: 0.1120 T22: 0.0651 REMARK 3 T33: 0.1456 T12: 0.0001 REMARK 3 T13: -0.0197 T23: -0.0007 REMARK 3 L TENSOR REMARK 3 L11: 4.3785 L22: 2.0463 REMARK 3 L33: 1.1826 L12: 1.6786 REMARK 3 L13: 0.3726 L23: 0.1274 REMARK 3 S TENSOR REMARK 3 S11: 0.0024 S12: -0.2137 S13: -0.2202 REMARK 3 S21: 0.1736 S22: -0.0618 S23: -0.2660 REMARK 3 S31: 0.0247 S32: 0.2170 S33: 0.0593 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 0 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 ORIGIN FOR THE GROUP (A): -0.3357 22.0252 -7.6304 REMARK 3 T TENSOR REMARK 3 T11: 0.0441 T22: 0.0523 REMARK 3 T33: 0.0227 T12: -0.0068 REMARK 3 T13: 0.0157 T23: -0.0267 REMARK 3 L TENSOR REMARK 3 L11: 2.5158 L22: 2.1733 REMARK 3 L33: 2.5387 L12: -0.3471 REMARK 3 L13: 0.6293 L23: -0.0273 REMARK 3 S TENSOR REMARK 3 S11: 0.0453 S12: 0.1952 S13: -0.1534 REMARK 3 S21: 0.0721 S22: -0.0711 S23: 0.1309 REMARK 3 S31: -0.0344 S32: -0.2250 S33: 0.0258 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 9LAD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-JAN-25. REMARK 100 THE DEPOSITION ID IS D_1300055298. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-OCT-24 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JUN 30, 2024 BUILT=20241002 REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29010 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 46.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 80.8 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 1.05100 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: PHASER 2.8.3 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1% W/V TRYPTONE, 0.001 M SODIUM AZIDE, REMARK 280 0.05 M HEPES SODIUM PH7.0, 12% W/V PEG 3,350., VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 46.78700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 59.11700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 46.78700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 59.11700 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: 1340 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -46.78700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 59.11700 REMARK 350 BIOMT3 2 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 HIS B 122 REMARK 465 HIS B 123 REMARK 465 HIS B 124 REMARK 465 HIS B 125 REMARK 465 HIS B 126 REMARK 465 GLY C 1 REMARK 465 ASP C 2 REMARK 465 ALA C 3 REMARK 465 ASP C 209 REMARK 465 LEU C 210 REMARK 465 ALA C 211 REMARK 465 ALA C 212 REMARK 465 ALA C 213 REMARK 465 HIS C 214 REMARK 465 HIS C 215 REMARK 465 HIS C 216 REMARK 465 HIS C 217 REMARK 465 HIS C 218 REMARK 465 HIS C 219 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 B 38 NE - CZ - NH2 ANGL. DEV. = -3.2 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 SER B 27 38.14 -156.86 REMARK 500 PRO B 41 123.07 -39.99 REMARK 500 ALA B 93 162.63 176.26 REMARK 500 ASN C 56 48.28 -105.87 REMARK 500 ASN C 65 33.50 -88.43 REMARK 500 PRO C 80 54.06 -90.17 REMARK 500 SER C 84 48.22 -102.35 REMARK 500 TRP C 120 -1.74 79.77 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 C 206 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 301 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 121 O REMARK 620 2 ASN C 56 OD1 53.2 REMARK 620 3 GLU C 134 OE1 52.1 3.0 REMARK 620 4 GLU C 134 OE2 53.3 4.2 1.8 REMARK 620 5 GLN C 135 O 53.4 0.8 2.4 3.4 REMARK 620 6 ASP C 136 OD1 56.3 4.0 4.2 3.4 3.5 REMARK 620 7 HOH C 471 O 56.3 3.1 5.3 5.5 3.2 3.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 134 OE2 REMARK 620 2 ASP C 136 OD1 74.4 REMARK 620 3 ASP C 136 OD2 119.5 50.0 REMARK 620 4 GLN C 146 OE1 82.1 156.4 148.4 REMARK 620 5 HOH C 408 O 154.0 128.0 86.4 75.4 REMARK 620 6 HOH C 444 O 83.8 86.8 72.7 88.6 108.0 REMARK 620 N 1 2 3 4 5 DBREF 9LAD B 1 126 PDB 9LAD 9LAD 1 126 DBREF 9LAD C 2 210 UNP P97738 NPTX2_RAT 224 432 SEQADV 9LAD GLY C 1 UNP P97738 EXPRESSION TAG SEQADV 9LAD ALA C 211 UNP P97738 EXPRESSION TAG SEQADV 9LAD ALA C 212 UNP P97738 EXPRESSION TAG SEQADV 9LAD ALA C 213 UNP P97738 EXPRESSION TAG SEQADV 9LAD HIS C 214 UNP P97738 EXPRESSION TAG SEQADV 9LAD HIS C 215 UNP P97738 EXPRESSION TAG SEQADV 9LAD HIS C 216 UNP P97738 EXPRESSION TAG SEQADV 9LAD HIS C 217 UNP P97738 EXPRESSION TAG SEQADV 9LAD HIS C 218 UNP P97738 EXPRESSION TAG SEQADV 9LAD HIS C 219 UNP P97738 EXPRESSION TAG SEQRES 1 B 126 GLN LEU GLN LEU VAL GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 126 ALA GLY ASP SER LEU LYS LEU SER CYS ILE ASP SER GLY SEQRES 3 B 126 SER THR PHE ASN LEU TYR ALA MET GLY TRP PHE ARG GLN SEQRES 4 B 126 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA SER ILE SER SEQRES 5 B 126 ARG GLY GLY GLY SER SER TYR TYR ALA ASP SER GLN LEU SEQRES 6 B 126 LYS GLY ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN SEQRES 7 B 126 THR VAL TYR LEU GLN MET ASN SER LEU LYS PRO GLU ASP SEQRES 8 B 126 THR ALA VAL TYR TYR CYS ASN ALA ARG ALA GLY ARG TYR SEQRES 9 B 126 ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 10 B 126 ALA ALA GLY HIS HIS HIS HIS HIS HIS SEQRES 1 C 219 GLY ASP ALA PHE LYS VAL SER LEU PRO LEU ARG THR ASN SEQRES 2 C 219 TYR LEU TYR GLY LYS ILE LYS LYS THR LEU PRO GLU LEU SEQRES 3 C 219 TYR ALA PHE THR ILE CYS LEU TRP LEU ARG SER SER ALA SEQRES 4 C 219 SER PRO GLY ILE GLY THR PRO PHE SER TYR ALA VAL PRO SEQRES 5 C 219 GLY GLN ALA ASN GLU ILE VAL LEU ILE GLU TRP GLY ASN SEQRES 6 C 219 ASN PRO ILE GLU LEU LEU ILE ASN ASP LYS VAL ALA GLN SEQRES 7 C 219 LEU PRO LEU PHE VAL SER ASP GLY LYS TRP HIS HIS ILE SEQRES 8 C 219 CYS ILE THR TRP THR THR ARG ASP GLY MET TRP GLU ALA SEQRES 9 C 219 PHE GLN ASP GLY GLU LYS LEU GLY THR GLY GLU ASN LEU SEQRES 10 C 219 ALA PRO TRP HIS PRO ILE LYS PRO GLY GLY VAL LEU ILE SEQRES 11 C 219 LEU GLY GLN GLU GLN ASP THR VAL GLY GLY ARG PHE ASP SEQRES 12 C 219 ALA THR GLN ALA PHE VAL GLY GLU LEU SER GLN PHE ASN SEQRES 13 C 219 ILE TRP ASP ARG VAL LEU ARG ALA GLN GLU ILE ILE ASN SEQRES 14 C 219 ILE ALA ASN CYS SER THR ASN MET PRO GLY ASN ILE ILE SEQRES 15 C 219 PRO TRP VAL ASP ASN ASN VAL ASP VAL PHE GLY GLY ALA SEQRES 16 C 219 SER LYS TRP PRO VAL GLU THR CYS GLU GLU ARG LEU LEU SEQRES 17 C 219 ASP LEU ALA ALA ALA HIS HIS HIS HIS HIS HIS HET AZI B 201 3 HET CA C 301 1 HET CA C 302 1 HET CL C 303 1 HET GOL C 304 6 HET CL C 305 1 HETNAM AZI AZIDE ION HETNAM CA CALCIUM ION HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 AZI N3 1- FORMUL 4 CA 2(CA 2+) FORMUL 6 CL 2(CL 1-) FORMUL 7 GOL C3 H8 O3 FORMUL 9 HOH *125(H2 O) HELIX 1 AA1 THR B 28 TYR B 32 5 5 HELIX 2 AA2 ASP B 62 ARG B 68 1 7 HELIX 3 AA3 ASN B 75 LYS B 77 5 3 HELIX 4 AA4 LYS B 88 THR B 92 5 5 HELIX 5 AA5 ARG C 98 GLY C 100 5 3 HELIX 6 AA6 ASP C 143 ALA C 147 5 5 HELIX 7 AA7 ARG C 163 ASN C 172 1 10 HELIX 8 AA8 VAL C 185 ASN C 187 5 3 HELIX 9 AA9 THR C 202 LEU C 208 1 7 SHEET 1 AA1 4 LEU B 4 SER B 7 0 SHEET 2 AA1 4 LEU B 18 ASP B 24 -1 O SER B 21 N SER B 7 SHEET 3 AA1 4 THR B 79 MET B 84 -1 O MET B 84 N LEU B 18 SHEET 4 AA1 4 PHE B 69 ASP B 74 -1 N SER B 72 O TYR B 81 SHEET 1 AA2 6 GLY B 10 GLN B 13 0 SHEET 2 AA2 6 THR B 111 SER B 116 1 O THR B 114 N VAL B 12 SHEET 3 AA2 6 ALA B 93 ALA B 101 -1 N ALA B 93 O VAL B 113 SHEET 4 AA2 6 ALA B 33 GLN B 39 -1 N ALA B 33 O ARG B 100 SHEET 5 AA2 6 GLU B 46 ILE B 51 -1 O GLU B 46 N ARG B 38 SHEET 6 AA2 6 SER B 58 TYR B 60 -1 O TYR B 59 N SER B 50 SHEET 1 AA3 4 GLY B 10 GLN B 13 0 SHEET 2 AA3 4 THR B 111 SER B 116 1 O THR B 114 N VAL B 12 SHEET 3 AA3 4 ALA B 93 ALA B 101 -1 N ALA B 93 O VAL B 113 SHEET 4 AA3 4 TYR B 104 TRP B 107 -1 O TYR B 106 N ALA B 99 SHEET 1 AA4 7 GLU C 109 GLY C 114 0 SHEET 2 AA4 7 MET C 101 GLN C 106 -1 N GLN C 106 O GLU C 109 SHEET 3 AA4 7 HIS C 89 THR C 96 -1 N CYS C 92 O PHE C 105 SHEET 4 AA4 7 ALA C 28 SER C 37 -1 N PHE C 29 O TRP C 95 SHEET 5 AA4 7 GLY C 150 TRP C 158 -1 O SER C 153 N TRP C 34 SHEET 6 AA4 7 LYS C 5 LEU C 8 -1 N LEU C 8 O GLY C 150 SHEET 7 AA4 7 SER C 196 TRP C 198 -1 O TRP C 198 N LYS C 5 SHEET 1 AA5 7 LYS C 75 GLN C 78 0 SHEET 2 AA5 7 GLU C 69 ILE C 72 -1 N LEU C 70 O ALA C 77 SHEET 3 AA5 7 GLN C 54 GLU C 62 -1 N ILE C 61 O GLU C 69 SHEET 4 AA5 7 GLY C 44 VAL C 51 -1 N TYR C 49 O ILE C 58 SHEET 5 AA5 7 VAL C 128 LEU C 131 -1 O ILE C 130 N SER C 48 SHEET 6 AA5 7 TYR C 16 ILE C 19 -1 N GLY C 17 O LEU C 131 SHEET 7 AA5 7 VAL C 189 PHE C 192 -1 O ASP C 190 N LYS C 18 SSBOND 1 CYS B 22 CYS B 97 1555 1555 2.25 SSBOND 2 CYS C 32 CYS C 92 1555 1555 2.10 SSBOND 3 CYS C 173 CYS C 203 1555 1555 1.82 LINK O HIS B 121 CA CA C 301 1555 4555 2.15 LINK OD1 ASN C 56 CA CA C 301 1555 1555 2.43 LINK OE1 GLU C 134 CA CA C 301 1555 1555 2.48 LINK OE2 GLU C 134 CA CA C 301 1555 1555 2.52 LINK OE2 GLU C 134 CA CA C 302 1555 1555 2.47 LINK O GLN C 135 CA CA C 301 1555 1555 2.25 LINK OD1 ASP C 136 CA CA C 301 1555 1555 2.37 LINK OD1 ASP C 136 CA CA C 302 1555 1555 2.54 LINK OD2 ASP C 136 CA CA C 302 1555 1555 2.69 LINK OE1 GLN C 146 CA CA C 302 1555 1555 2.48 LINK CA CA C 301 O HOH C 471 1555 1555 2.52 LINK CA CA C 302 O HOH C 408 1555 1555 2.41 LINK CA CA C 302 O HOH C 444 1555 1555 2.22 CRYST1 93.574 118.234 39.464 90.00 90.00 90.00 P 21 21 2 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 0.010687 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025340 0.00000 CONECT 152 750 CONECT 750 152 CONECT 1172 1640 CONECT 1346 2569 CONECT 1640 1172 CONECT 1974 2569 CONECT 1975 2569 2570 CONECT 1979 2569 CONECT 1991 2569 2570 CONECT 1992 2570 CONECT 2064 2570 CONECT 2284 2519 CONECT 2519 2284 CONECT 2566 2567 CONECT 2567 2566 2568 CONECT 2568 2567 CONECT 2569 1346 1974 1975 1979 CONECT 2569 1991 2685 CONECT 2570 1975 1991 1992 2064 CONECT 2570 2621 2657 CONECT 2572 2573 2574 CONECT 2573 2572 CONECT 2574 2572 2575 2576 CONECT 2575 2574 CONECT 2576 2574 2577 CONECT 2577 2576 CONECT 2621 2570 CONECT 2657 2570 CONECT 2685 2569 MASTER 392 0 6 9 28 0 0 6 2680 2 29 27 END