PDB Short entry for 4DGI HEADER PROTEIN BINDING 26-JAN-12 4DGI TITLE STRUCTURE OF POM1 FAB FRAGMENT COMPLEXED WITH HUMAN PRPC FRAGMENT 120- TITLE 2 230 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR PRION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 120-230; COMPND 5 SYNONYM: PRP, ASCR, PRP27-30, PRP33-35C; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: POM1 FAB HEAVY CHAIN; COMPND 9 CHAIN: H; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: POM1 FAB LIGHT CHAIN; COMPND 12 CHAIN: L SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: PRNP, PRIP, PRP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 13 ORGANISM_TAXID: 10090 KEYWDS PRION, ANTIBODY, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR P.K.BARAL,B.WIELAND,M.SWAYAMPAKULA,M.N.JAMES REVDAT 2 23-JAN-13 4DGI 1 JRNL REVDAT 1 31-OCT-12 4DGI 0 JRNL AUTH P.K.BARAL,B.WIELAND,M.SWAYAMPAKULA,M.POLYMENIDOU,M.H.RAHMAN, JRNL AUTH 2 N.N.KAV,A.AGUZZI,M.N.JAMES JRNL TITL STRUCTURAL STUDIES ON THE FOLDED DOMAIN OF THE HUMAN PRION JRNL TITL 2 PROTEIN BOUND TO THE FAB FRAGMENT OF THE ANTIBODY POM1. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 68 1501 2012 JRNL REFN ISSN 0907-4449 JRNL PMID 23090399 JRNL DOI 10.1107/S0907444912037328 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH P.K.BARAL,B.WIELAND,M.SWAYAMPAKULA,M.POLYMENIDOU,A.AGUZZI, REMARK 1 AUTH 2 N.N.KAV,M.N.JAMES REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DIFFRACTION ANALYSIS REMARK 1 TITL 2 OF PRION PROTEIN BOUND TO THE FAB FRAGMENT OF THE POM1 REMARK 1 TITL 3 ANTIBODY. REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 67 1211 2011 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 22102029 REMARK 1 DOI 10.1107/S1744309111026273 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.19 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.420 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 25651 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.259 REMARK 3 R VALUE (WORKING SET) : 0.258 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 1285 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.1982 - 4.9881 0.97 2687 159 0.2692 0.2892 REMARK 3 2 4.9881 - 3.9610 1.00 2687 169 0.2010 0.2348 REMARK 3 3 3.9610 - 3.4608 1.00 2746 148 0.2238 0.2473 REMARK 3 4 3.4608 - 3.1446 1.00 2726 148 0.2276 0.2914 REMARK 3 5 3.1446 - 2.9193 1.00 2704 131 0.2419 0.3170 REMARK 3 6 2.9193 - 2.7473 0.99 2707 143 0.2794 0.3591 REMARK 3 7 2.7473 - 2.6097 0.99 2692 118 0.3173 0.3467 REMARK 3 8 2.6097 - 2.4961 0.99 2752 121 0.3685 0.3492 REMARK 3 9 2.4961 - 2.4000 0.99 2665 148 0.4166 0.4133 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 51.45 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.890 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.16600 REMARK 3 B22 (A**2) : 15.78090 REMARK 3 B33 (A**2) : -13.61490 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.40840 REMARK 3 B23 (A**2) : -0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.018 4209 REMARK 3 ANGLE : 2.045 5715 REMARK 3 CHIRALITY : 0.109 628 REMARK 3 PLANARITY : 0.014 736 REMARK 3 DIHEDRAL : 13.056 1519 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4DGI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JAN-12. REMARK 100 THE RCSB ID CODE IS RCSB070299. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.56 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26309 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 76.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.19000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.78000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.300 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 0.1M MES, 0.1M SODIUM REMARK 280 ACETATE, PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 41.76500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 52.96000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.76500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 52.96000 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, H, L 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 ALA A 120 REMARK 465 VAL A 121 REMARK 465 VAL A 122 REMARK 465 GLY A 123 REMARK 465 GLY A 124 REMARK 465 LEU A 125 REMARK 465 GLN A 223 REMARK 465 ALA A 224 REMARK 465 TYR A 225 REMARK 465 TYR A 226 REMARK 465 GLN A 227 REMARK 465 ARG A 228 REMARK 465 GLY A 229 REMARK 465 SER A 230 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY H 135 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 OE1 GLU H 153 O HOH H 361 1.93 REMARK 500 O HOH H 324 O HOH H 398 2.14 REMARK 500 O HOH H 330 O HOH H 383 2.16 REMARK 500 O HOH H 356 O HOH H 398 2.17 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 NH1 ARG A 164 OD1 ASN L 76 3455 2.05 REMARK 500 O HOH L 425 O HOH L 443 2555 2.13 REMARK 500 O HOH A 317 O HOH H 390 2554 2.13 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 A 208 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 MET H 20 CG - SD - CE ANGL. DEV. = -10.1 DEGREES REMARK 500 LYS H 65 CD - CE - NZ ANGL. DEV. = 15.8 DEGREES REMARK 500 PRO H 132 C - N - CA ANGL. DEV. = -11.3 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 PRO A 165 155.88 -47.48 REMARK 500 ASN A 171 -178.01 -178.09 REMARK 500 GLU A 196 162.41 69.37 REMARK 500 THR H 137 -156.29 -76.39 REMARK 500 SER H 139 -5.89 59.71 REMARK 500 SER H 165 20.34 -146.25 REMARK 500 ALA L 51 -43.12 70.74 REMARK 500 ALA L 84 172.84 178.58 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH H 389 DISTANCE = 7.76 ANGSTROMS REMARK 525 HOH L 444 DISTANCE = 5.06 ANGSTROMS 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 NA L 300 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU L 81 OE1 REMARK 620 2 GLU L 79 OE1 54.1 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA L 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W9E RELATED DB: PDB REMARK 900 STRUCTURE OF ICSM 18 (ANTI-PRP THERAPEUTIC ANTIBODY) FAB REMARK 900 FRAGMENT COMPLEXED WITH HUMAN PRP FRAGMENT 119-231 REMARK 900 RELATED ID: 1TQB RELATED DB: PDB REMARK 900 OVINE RECOMBINANT PRP(114-234), VRQ VARIANT IN COMPLEX WITH REMARK 900 THE FAB OF THE VRQ14 ANTIBODY DBREF 4DGI A 120 230 UNP P04156 PRIO_HUMAN 120 230 DBREF 4DGI H 1 218 PDB 4DGI 4DGI 1 218 DBREF 4DGI L 1 213 PDB 4DGI 4DGI 1 213 SEQRES 1 A 111 ALA VAL VAL GLY GLY LEU GLY GLY TYR MET LEU GLY SER SEQRES 2 A 111 ALA MET SER ARG PRO ILE ILE HIS PHE GLY SER ASP TYR SEQRES 3 A 111 GLU ASP ARG TYR TYR ARG GLU ASN MET HIS ARG TYR PRO SEQRES 4 A 111 ASN GLN VAL TYR TYR ARG PRO MET ASP GLU TYR SER ASN SEQRES 5 A 111 GLN ASN ASN PHE VAL HIS ASP CYS VAL ASN ILE THR ILE SEQRES 6 A 111 LYS GLN HIS THR VAL THR THR THR THR LYS GLY GLU ASN SEQRES 7 A 111 PHE THR GLU THR ASP VAL LYS MET MET GLU ARG VAL VAL SEQRES 8 A 111 GLU GLN MET CYS ILE THR GLN TYR GLU ARG GLU SER GLN SEQRES 9 A 111 ALA TYR TYR GLN ARG GLY SER SEQRES 1 H 218 GLN VAL GLN LEU GLN GLN SER GLY THR GLU LEU VAL MET SEQRES 2 H 218 PRO GLY ALA SER VAL LYS MET SER CYS LYS ALA SER GLY SEQRES 3 H 218 TYR THR PHE THR ASP TYR TRP MET HIS TRP VAL LYS GLN SEQRES 4 H 218 ARG PRO GLY GLN GLY LEU GLU TRP ILE GLY SER ILE ASP SEQRES 5 H 218 PRO SER ASP SER TYR THR SER HIS ASN GLU LYS PHE LYS SEQRES 6 H 218 GLY LYS ALA THR LEU THR VAL ASP GLU SER SER SER THR SEQRES 7 H 218 ALA TYR MET GLN LEU SER SER LEU THR SER GLU ASP SER SEQRES 8 H 218 ALA VAL TYR PHE CYS SER ARG SER GLY TYR GLY TYR TYR SEQRES 9 H 218 ALA MET GLU TYR TRP GLY GLN GLY THR SER VAL THR VAL SEQRES 10 H 218 SER SER ALA LYS THR THR PRO PRO SER VAL TYR PRO LEU SEQRES 11 H 218 ALA PRO GLY GLY GLY ALA THR ASN SER MET VAL THR LEU SEQRES 12 H 218 GLY CYS LEU VAL LYS GLY TYR PHE PRO GLU PRO VAL THR SEQRES 13 H 218 VAL THR TRP ASN SER GLY SER LEU SER GLY GLY VAL HIS SEQRES 14 H 218 THR PHE PRO ALA VAL LEU GLN SER ASP LEU TYR THR LEU SEQRES 15 H 218 SER SER SER VAL THR VAL PRO SER SER THR TRP PRO SER SEQRES 16 H 218 GLU THR VAL THR CYS ASN VAL ALA HIS PRO ALA SER SER SEQRES 17 H 218 THR LYS VAL ASP LYS LYS ILE VAL PRO ARG SEQRES 1 L 213 ASP ILE VAL LEU THR GLN SER PRO ALA ILE LEU SER VAL SEQRES 2 L 213 SER PRO GLY GLU ARG VAL SER PHE SER CYS ARG ALA SER SEQRES 3 L 213 GLN ASN ILE GLY THR SER ILE HIS TRP TYR GLN GLN ARG SEQRES 4 L 213 THR ASN GLU SER PRO ARG LEU ILE ILE LYS TYR ALA SER SEQRES 5 L 213 GLU SER ILE SER GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 L 213 GLY SER GLY THR ASP PHE THR LEU SER ILE ASN SER VAL SEQRES 7 L 213 GLU SER GLU ASP ILE ALA ASP TYR TYR CYS GLN GLN SER SEQRES 8 L 213 ASN THR TRP PRO TYR THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 213 GLU LEU LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE SEQRES 10 L 213 PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SEQRES 11 L 213 SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP SEQRES 12 L 213 ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN SEQRES 13 L 213 ASN GLY VAL LEU ASN SER GLU THR ASP GLN ASP SER LYS SEQRES 14 L 213 ASP SER THR TYR SER MET SER SER THR LEU THR LEU THR SEQRES 15 L 213 LYS ASP GLU TYR GLU ARG HIS ASN THR TYR THR CYS GLU SEQRES 16 L 213 ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER SEQRES 17 L 213 PHE ASN ARG ASN GLU HET NA L 300 1 HETNAM NA SODIUM ION FORMUL 4 NA NA 1+ FORMUL 5 HOH *170(H2 O) HELIX 1 1 SER A 143 MET A 154 1 12 HELIX 2 2 HIS A 155 TYR A 157 5 3 HELIX 3 3 PRO A 165 TYR A 169 5 5 HELIX 4 4 ASN A 171 LYS A 194 1 24 HELIX 5 5 THR A 199 SER A 222 1 24 HELIX 6 6 THR H 28 TYR H 32 5 5 HELIX 7 7 GLU H 62 LYS H 65 5 4 HELIX 8 8 GLU H 74 SER H 76 5 3 HELIX 9 9 THR H 87 SER H 91 5 5 HELIX 10 10 PRO H 205 SER H 208 5 4 HELIX 11 11 GLU L 79 ILE L 83 5 5 HELIX 12 12 SER L 121 SER L 127 1 7 HELIX 13 13 LYS L 183 ARG L 188 1 6 SHEET 1 A 2 MET A 129 LEU A 130 0 SHEET 2 A 2 TYR A 162 TYR A 163 -1 O TYR A 163 N MET A 129 SHEET 1 B 4 GLN H 3 GLN H 6 0 SHEET 2 B 4 VAL H 18 SER H 25 -1 O LYS H 23 N GLN H 5 SHEET 3 B 4 THR H 78 LEU H 83 -1 O LEU H 83 N VAL H 18 SHEET 4 B 4 ALA H 68 ASP H 73 -1 N THR H 71 O TYR H 80 SHEET 1 C 6 THR H 9 VAL H 12 0 SHEET 2 C 6 THR H 113 VAL H 117 1 O THR H 116 N GLU H 10 SHEET 3 C 6 ALA H 92 SER H 99 -1 N ALA H 92 O VAL H 115 SHEET 4 C 6 MET H 34 GLN H 39 -1 N HIS H 35 O SER H 97 SHEET 5 C 6 LEU H 45 ILE H 51 -1 O GLU H 46 N LYS H 38 SHEET 6 C 6 THR H 58 HIS H 60 -1 O SER H 59 N SER H 50 SHEET 1 D 4 THR H 9 VAL H 12 0 SHEET 2 D 4 THR H 113 VAL H 117 1 O THR H 116 N GLU H 10 SHEET 3 D 4 ALA H 92 SER H 99 -1 N ALA H 92 O VAL H 115 SHEET 4 D 4 MET H 106 TRP H 109 -1 O TYR H 108 N ARG H 98 SHEET 1 E 4 SER H 126 LEU H 130 0 SHEET 2 E 4 MET H 140 TYR H 150 -1 O LEU H 146 N TYR H 128 SHEET 3 E 4 LEU H 179 PRO H 189 -1 O LEU H 182 N VAL H 147 SHEET 4 E 4 VAL H 168 THR H 170 -1 N HIS H 169 O SER H 185 SHEET 1 F 4 SER H 126 LEU H 130 0 SHEET 2 F 4 MET H 140 TYR H 150 -1 O LEU H 146 N TYR H 128 SHEET 3 F 4 LEU H 179 PRO H 189 -1 O LEU H 182 N VAL H 147 SHEET 4 F 4 VAL H 174 GLN H 176 -1 N GLN H 176 O LEU H 179 SHEET 1 G 3 THR H 156 TRP H 159 0 SHEET 2 G 3 THR H 199 HIS H 204 -1 O ALA H 203 N THR H 156 SHEET 3 G 3 THR H 209 LYS H 214 -1 O THR H 209 N HIS H 204 SHEET 1 H 4 LEU L 4 SER L 7 0 SHEET 2 H 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 H 4 ASP L 70 ILE L 75 -1 O ILE L 75 N VAL L 19 SHEET 4 H 4 PHE L 62 GLY L 66 -1 N SER L 63 O SER L 74 SHEET 1 I 6 ILE L 10 VAL L 13 0 SHEET 2 I 6 THR L 102 LEU L 106 1 O GLU L 105 N VAL L 13 SHEET 3 I 6 ASP L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 I 6 ILE L 33 GLN L 38 -1 N GLN L 38 O ASP L 85 SHEET 5 I 6 ARG L 45 LYS L 49 -1 O ARG L 45 N GLN L 37 SHEET 6 I 6 GLU L 53 SER L 54 -1 O GLU L 53 N LYS L 49 SHEET 1 J 4 ILE L 10 VAL L 13 0 SHEET 2 J 4 THR L 102 LEU L 106 1 O GLU L 105 N VAL L 13 SHEET 3 J 4 ASP L 85 GLN L 90 -1 N TYR L 86 O THR L 102 SHEET 4 J 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 K 4 THR L 114 PHE L 118 0 SHEET 2 K 4 GLY L 129 PHE L 139 -1 O VAL L 133 N PHE L 118 SHEET 3 K 4 TYR L 173 THR L 182 -1 O MET L 175 N LEU L 136 SHEET 4 K 4 VAL L 159 GLU L 163 -1 N LEU L 160 O THR L 178 SHEET 1 L 4 SER L 153 ARG L 155 0 SHEET 2 L 4 ILE L 144 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 L 4 THR L 191 HIS L 198 -1 O GLU L 195 N LYS L 147 SHEET 4 L 4 ILE L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SSBOND 1 CYS A 179 CYS A 214 1555 1555 2.05 SSBOND 2 CYS H 22 CYS H 96 1555 1555 2.10 SSBOND 3 CYS H 145 CYS H 200 1555 1555 2.04 SSBOND 4 CYS L 23 CYS L 88 1555 1555 2.05 SSBOND 5 CYS L 134 CYS L 194 1555 1555 2.03 LINK OE1 GLU L 81 NA NA L 300 1555 1555 2.49 LINK OE1 GLU L 79 NA NA L 300 1555 1555 2.52 CISPEP 1 GLY A 126 GLY A 127 0 2.64 CISPEP 2 PHE H 151 PRO H 152 0 -3.19 CISPEP 3 GLU H 153 PRO H 154 0 0.53 CISPEP 4 TRP H 193 PRO H 194 0 5.64 CISPEP 5 SER L 7 PRO L 8 0 -8.08 CISPEP 6 TRP L 94 PRO L 95 0 -3.93 CISPEP 7 TYR L 140 PRO L 141 0 1.49 SITE 1 AC1 5 SER H 191 SER H 195 GLU H 196 GLU L 79 SITE 2 AC1 5 GLU L 81 CRYST1 83.530 105.920 76.230 90.00 95.08 90.00 C 1 2 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 0.011972 0.000000 0.001064 0.00000 SCALE2 0.000000 0.009441 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013170 0.00000