HEADER IMMUNE SYSTEM 08-FEB-18 6CDM TITLE STRUCTURE OF VACCINE-ELICITED HIV-1 NEUTRALIZING ANTIBODY VFP7.04 IN TITLE 2 COMPLEX WITH HIV-1 FUSION PEPTIDE RESIDUE 512-519 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VFP7.04 HEAVY CHAIN; COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VFP7.04 LIGHT CHAIN; COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: HIV FUSION PEPTIDE (512-519); COMPND 11 CHAIN: C, F; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_TAXID: 10090; SOURCE 4 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_TAXID: 10090; SOURCE 9 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 11 MOL_ID: 3; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 14 ORGANISM_TAXID: 11676 KEYWDS NEUTRALIZING, ANTIBODY, FUSION PEPTIDE, COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR K.XU,K.LIU,P.D.KWONG REVDAT 3 04-OCT-23 6CDM 1 REMARK REVDAT 2 20-JUN-18 6CDM 1 JRNL REVDAT 1 16-MAY-18 6CDM 0 JRNL AUTH K.XU,P.ACHARYA,R.KONG,C.CHENG,G.Y.CHUANG,K.LIU,M.K.LOUDER, JRNL AUTH 2 S.O'DELL,R.RAWI,M.SASTRY,C.H.SHEN,B.ZHANG,T.ZHOU,M.ASOKAN, JRNL AUTH 3 R.T.BAILER,M.CHAMBERS,X.CHEN,C.W.CHOI,V.P.DANDEY, JRNL AUTH 4 N.A.DORIA-ROSE,A.DRUZ,E.T.ENG,S.K.FARNEY,K.E.FOULDS,H.GENG, JRNL AUTH 5 I.S.GEORGIEV,J.GORMAN,K.R.HILL,A.J.JAFARI,Y.D.KWON,Y.T.LAI, JRNL AUTH 6 T.LEMMIN,K.MCKEE,T.Y.OHR,L.OU,D.PENG,A.P.ROWSHAN,Z.SHENG, JRNL AUTH 7 J.P.TODD,Y.TSYBOVSKY,E.G.VIOX,Y.WANG,H.WEI,Y.YANG,A.F.ZHOU, JRNL AUTH 8 R.CHEN,L.YANG,D.G.SCORPIO,A.B.MCDERMOTT,L.SHAPIRO, JRNL AUTH 9 B.CARRAGHER,C.S.POTTER,J.R.MASCOLA,P.D.KWONG JRNL TITL EPITOPE-BASED VACCINE DESIGN YIELDS FUSION PEPTIDE-DIRECTED JRNL TITL 2 ANTIBODIES THAT NEUTRALIZE DIVERSE STRAINS OF HIV-1. JRNL REF NAT. MED. V. 24 857 2018 JRNL REFN ISSN 1546-170X JRNL PMID 29867235 JRNL DOI 10.1038/S41591-018-0042-6 REMARK 2 REMARK 2 RESOLUTION. 2.41 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.41 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.42 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 32997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.740 REMARK 3 FREE R VALUE TEST SET COUNT : 1565 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 48.4270 - 5.3525 1.00 2959 165 0.2096 0.2306 REMARK 3 2 5.3525 - 4.2492 1.00 2928 134 0.1641 0.1596 REMARK 3 3 4.2492 - 3.7123 1.00 2892 129 0.1655 0.2255 REMARK 3 4 3.7123 - 3.3730 1.00 2866 135 0.1625 0.2047 REMARK 3 5 3.3730 - 3.1313 1.00 2877 151 0.1728 0.2044 REMARK 3 6 3.1313 - 2.9467 1.00 2816 165 0.1896 0.2328 REMARK 3 7 2.9467 - 2.7991 1.00 2895 136 0.1938 0.2642 REMARK 3 8 2.7991 - 2.6773 1.00 2856 132 0.2025 0.2527 REMARK 3 9 2.6773 - 2.5742 1.00 2868 129 0.2041 0.2668 REMARK 3 10 2.5742 - 2.4854 0.99 2813 166 0.2048 0.2569 REMARK 3 11 2.4854 - 2.4077 0.93 2662 123 0.2208 0.2816 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.370 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.57 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.005 6888 REMARK 3 ANGLE : 0.911 9372 REMARK 3 CHIRALITY : 0.054 1066 REMARK 3 PLANARITY : 0.005 1184 REMARK 3 DIHEDRAL : 8.724 4076 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 : 3 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN A REMARK 3 SELECTION : CHAIN D REMARK 3 ATOM PAIRS NUMBER : 1996 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN C REMARK 3 SELECTION : CHAIN F REMARK 3 ATOM PAIRS NUMBER : 36 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 3 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN B REMARK 3 SELECTION : CHAIN E REMARK 3 ATOM PAIRS NUMBER : 1993 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6CDM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-FEB-18. REMARK 100 THE DEPOSITION ID IS D_1000232578. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-NOV-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 : APS REMARK 200 BEAMLINE : 22-ID 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 : 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33013 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.9000 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) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.41200 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: 3BKY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0, 30% PEG 6000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, 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 30.51700 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, 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 LYS A 214 REMARK 465 SER A 215 REMARK 465 CYS A 216 REMARK 465 CYS B 214 REMARK 465 VAL C 518 REMARK 465 PHE C 519 REMARK 465 LYS D 214 REMARK 465 SER D 215 REMARK 465 CYS D 216 REMARK 465 CYS E 214 REMARK 465 VAL F 518 REMARK 465 PHE F 519 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 HOH A 379 O HOH D 309 1.85 REMARK 500 NZ LYS B 207 O HOH B 301 1.87 REMARK 500 O HOH D 397 O HOH D 398 1.91 REMARK 500 O HOH A 320 O HOH B 375 1.94 REMARK 500 O HOH A 326 O HOH A 390 1.94 REMARK 500 OE2 GLU E 79 OE2 GLU E 81 1.96 REMARK 500 O HOH E 375 O HOH E 376 1.98 REMARK 500 O GLU B 213 O HOH B 302 2.02 REMARK 500 O HOH A 356 O HOH A 378 2.03 REMARK 500 O HOH B 333 O HOH B 334 2.04 REMARK 500 OD2 ASP D 72 O HOH D 301 2.04 REMARK 500 O TYR B 96 O HOH B 303 2.05 REMARK 500 O HOH D 321 O HOH D 391 2.06 REMARK 500 NE2 GLN A 1 O HOH A 301 2.07 REMARK 500 O HOH D 368 O HOH E 371 2.09 REMARK 500 O HOH E 336 O HOH E 372 2.10 REMARK 500 O HOH D 336 O HOH D 365 2.13 REMARK 500 O HOH D 345 O HOH D 363 2.14 REMARK 500 O HOH D 392 O HOH E 329 2.14 REMARK 500 O HOH E 351 O HOH E 358 2.15 REMARK 500 O HOH E 342 O HOH E 364 2.15 REMARK 500 OE1 GLN A 39 O HOH A 302 2.15 REMARK 500 O HOH B 305 O HOH B 371 2.17 REMARK 500 O HOH E 360 O HOH E 361 2.18 REMARK 500 N ARG E 77 O HOH E 301 2.19 REMARK 500 OE1 GLU B 81 O HOH B 304 2.19 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 O HOH A 382 O HOH A 394 2548 1.86 REMARK 500 O HOH A 352 O HOH A 385 2658 1.97 REMARK 500 O HOH D 312 O HOH E 347 2649 2.04 REMARK 500 O HOH A 341 O HOH A 354 2548 2.12 REMARK 500 OE2 GLU D 148 OG SER D 187 2659 2.17 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 GLU E 105 CA - CB - CG ANGL. DEV. = 14.0 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 ALA A 88 -178.03 -173.09 REMARK 500 TRP A 99 -127.56 -111.48 REMARK 500 VAL B 51 -54.67 73.89 REMARK 500 ASN B 152 -5.83 71.68 REMARK 500 ALA D 88 -177.33 -173.60 REMARK 500 TRP D 99 -127.76 -108.66 REMARK 500 VAL E 51 -53.33 73.94 REMARK 500 ASN E 152 -3.84 69.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5TKJ RELATED DB: PDB REMARK 900 PDB ENTRY FOR THE SAME CITATION DBREF 6CDM A 1 216 PDB 6CDM 6CDM 1 216 DBREF 6CDM B 1 214 PDB 6CDM 6CDM 1 214 DBREF 6CDM C 512 519 PDB 6CDM 6CDM 512 519 DBREF 6CDM D 1 216 PDB 6CDM 6CDM 1 216 DBREF 6CDM E 1 214 PDB 6CDM 6CDM 1 214 DBREF 6CDM F 512 519 PDB 6CDM 6CDM 512 519 SEQRES 1 A 221 GLN VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 A 221 PRO GLY ALA SER VAL THR LEU SER CYS LYS ALA SER GLY SEQRES 3 A 221 TYR THR PHE THR ASP TYR GLU MET HIS TRP VAL LYS GLN SEQRES 4 A 221 THR PRO VAL HIS GLY LEU GLU TRP ILE GLY ALA ILE VAL SEQRES 5 A 221 PRO GLU THR GLY PHE THR ALA TYR THR GLN LYS PHE LYS SEQRES 6 A 221 GLY LYS ALA MET LEU THR ALA ASP LYS SER SER SER THR SEQRES 7 A 221 ALA TYR MET GLU LEU ARG SER LEU THR SER GLU ASP SER SEQRES 8 A 221 ALA VAL TYR PHE CYS SER ARG LEU ARG LEU TYR TRP TYR SEQRES 9 A 221 PHE ASP VAL TRP GLY THR GLY THR THR VAL THR VAL SER SEQRES 10 A 221 SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 11 A 221 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 12 A 221 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 13 A 221 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 14 A 221 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 15 A 221 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 16 A 221 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 17 A 221 ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 B 219 GLY VAL LEU MET THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 B 219 ARG LEU GLY ASP GLN ALA SER ILE SER CYS ARG SER SER SEQRES 3 B 219 GLN SER ILE VAL TYR SER ASN GLY ASN THR TYR LEU GLU SEQRES 4 B 219 TRP TYR LEU GLN ARG PRO GLY GLN SER PRO LYS LEU LEU SEQRES 5 B 219 ILE TYR LYS VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 B 219 ARG VAL SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 B 219 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 B 219 TYR CYS PHE GLN GLY SER HIS VAL PRO TYR THR PHE GLY SEQRES 9 B 219 GLY GLY THR LYS LEU GLU ILE LYS ARG THR VAL ALA ALA SEQRES 10 B 219 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU SEQRES 11 B 219 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN SEQRES 12 B 219 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP SEQRES 13 B 219 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR SEQRES 14 B 219 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER SEQRES 15 B 219 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS SEQRES 16 B 219 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER SEQRES 17 B 219 PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 C 8 ALA VAL GLY ILE GLY ALA VAL PHE SEQRES 1 D 221 GLN VAL GLN LEU GLN GLN SER GLY ALA GLU LEU VAL ARG SEQRES 2 D 221 PRO GLY ALA SER VAL THR LEU SER CYS LYS ALA SER GLY SEQRES 3 D 221 TYR THR PHE THR ASP TYR GLU MET HIS TRP VAL LYS GLN SEQRES 4 D 221 THR PRO VAL HIS GLY LEU GLU TRP ILE GLY ALA ILE VAL SEQRES 5 D 221 PRO GLU THR GLY PHE THR ALA TYR THR GLN LYS PHE LYS SEQRES 6 D 221 GLY LYS ALA MET LEU THR ALA ASP LYS SER SER SER THR SEQRES 7 D 221 ALA TYR MET GLU LEU ARG SER LEU THR SER GLU ASP SER SEQRES 8 D 221 ALA VAL TYR PHE CYS SER ARG LEU ARG LEU TYR TRP TYR SEQRES 9 D 221 PHE ASP VAL TRP GLY THR GLY THR THR VAL THR VAL SER SEQRES 10 D 221 SER ALA SER THR LYS GLY PRO SER VAL PHE PRO LEU ALA SEQRES 11 D 221 PRO SER SER LYS SER THR SER GLY GLY THR ALA ALA LEU SEQRES 12 D 221 GLY CYS LEU VAL LYS ASP TYR PHE PRO GLU PRO VAL THR SEQRES 13 D 221 VAL SER TRP ASN SER GLY ALA LEU THR SER GLY VAL HIS SEQRES 14 D 221 THR PHE PRO ALA VAL LEU GLN SER SER GLY LEU TYR SER SEQRES 15 D 221 LEU SER SER VAL VAL THR VAL PRO SER SER SER LEU GLY SEQRES 16 D 221 THR GLN THR TYR ILE CYS ASN VAL ASN HIS LYS PRO SER SEQRES 17 D 221 ASN THR LYS VAL ASP LYS LYS VAL GLU PRO LYS SER CYS SEQRES 1 E 219 GLY VAL LEU MET THR GLN THR PRO LEU SER LEU PRO VAL SEQRES 2 E 219 ARG LEU GLY ASP GLN ALA SER ILE SER CYS ARG SER SER SEQRES 3 E 219 GLN SER ILE VAL TYR SER ASN GLY ASN THR TYR LEU GLU SEQRES 4 E 219 TRP TYR LEU GLN ARG PRO GLY GLN SER PRO LYS LEU LEU SEQRES 5 E 219 ILE TYR LYS VAL SER ASN ARG PHE SER GLY VAL PRO ASP SEQRES 6 E 219 ARG VAL SER GLY SER GLY SER GLY THR ASP PHE THR LEU SEQRES 7 E 219 LYS ILE SER ARG VAL GLU ALA GLU ASP LEU GLY VAL TYR SEQRES 8 E 219 TYR CYS PHE GLN GLY SER HIS VAL PRO TYR THR PHE GLY SEQRES 9 E 219 GLY GLY THR LYS LEU GLU ILE LYS ARG THR VAL ALA ALA SEQRES 10 E 219 PRO SER VAL PHE ILE PHE PRO PRO SER ASP GLU GLN LEU SEQRES 11 E 219 LYS SER GLY THR ALA SER VAL VAL CYS LEU LEU ASN ASN SEQRES 12 E 219 PHE TYR PRO ARG GLU ALA LYS VAL GLN TRP LYS VAL ASP SEQRES 13 E 219 ASN ALA LEU GLN SER GLY ASN SER GLN GLU SER VAL THR SEQRES 14 E 219 GLU GLN ASP SER LYS ASP SER THR TYR SER LEU SER SER SEQRES 15 E 219 THR LEU THR LEU SER LYS ALA ASP TYR GLU LYS HIS LYS SEQRES 16 E 219 VAL TYR ALA CYS GLU VAL THR HIS GLN GLY LEU SER SER SEQRES 17 E 219 PRO VAL THR LYS SER PHE ASN ARG GLY GLU CYS SEQRES 1 F 8 ALA VAL GLY ILE GLY ALA VAL PHE FORMUL 7 HOH *351(H2 O) HELIX 1 AA1 THR A 28 TYR A 32 5 5 HELIX 2 AA2 GLN A 61 LYS A 64 5 4 HELIX 3 AA3 THR A 83 SER A 87 5 5 HELIX 4 AA4 SER A 127 LYS A 129 5 3 HELIX 5 AA5 SER A 156 ALA A 158 5 3 HELIX 6 AA6 LYS A 201 ASN A 204 5 4 HELIX 7 AA7 GLU B 79 LEU B 83 5 5 HELIX 8 AA8 SER B 121 LYS B 126 1 6 HELIX 9 AA9 LYS B 183 GLU B 187 1 5 HELIX 10 AB1 THR D 28 TYR D 32 5 5 HELIX 11 AB2 GLN D 61 LYS D 64 5 4 HELIX 12 AB3 THR D 83 SER D 87 5 5 HELIX 13 AB4 SER D 127 LYS D 129 5 3 HELIX 14 AB5 SER D 156 ALA D 158 5 3 HELIX 15 AB6 LYS D 201 ASN D 204 5 4 HELIX 16 AB7 GLU E 79 LEU E 83 5 5 HELIX 17 AB8 SER E 121 SER E 127 1 7 HELIX 18 AB9 LYS E 183 GLU E 187 1 5 SHEET 1 AA1 4 GLN A 3 GLN A 6 0 SHEET 2 AA1 4 VAL A 18 SER A 25 -1 O LYS A 23 N GLN A 5 SHEET 3 AA1 4 THR A 77 LEU A 82 -1 O MET A 80 N LEU A 20 SHEET 4 AA1 4 ALA A 67 ASP A 72 -1 N THR A 70 O TYR A 79 SHEET 1 AA2 6 GLU A 10 VAL A 12 0 SHEET 2 AA2 6 THR A 107 VAL A 111 1 O THR A 108 N GLU A 10 SHEET 3 AA2 6 ALA A 88 LEU A 95 -1 N TYR A 90 O THR A 107 SHEET 4 AA2 6 GLU A 33 THR A 40 -1 N HIS A 35 O SER A 93 SHEET 5 AA2 6 GLY A 44 ILE A 51 -1 O GLU A 46 N LYS A 38 SHEET 6 AA2 6 THR A 57 TYR A 59 -1 O ALA A 58 N ALA A 50 SHEET 1 AA3 4 SER A 120 LEU A 124 0 SHEET 2 AA3 4 THR A 135 TYR A 145 -1 O LEU A 141 N PHE A 122 SHEET 3 AA3 4 TYR A 176 PRO A 185 -1 O VAL A 184 N ALA A 136 SHEET 4 AA3 4 VAL A 163 THR A 165 -1 N HIS A 164 O VAL A 181 SHEET 1 AA4 4 THR A 131 SER A 132 0 SHEET 2 AA4 4 THR A 135 TYR A 145 -1 O THR A 135 N SER A 132 SHEET 3 AA4 4 TYR A 176 PRO A 185 -1 O VAL A 184 N ALA A 136 SHEET 4 AA4 4 VAL A 169 LEU A 170 -1 N VAL A 169 O SER A 177 SHEET 1 AA5 3 THR A 151 TRP A 154 0 SHEET 2 AA5 3 TYR A 194 HIS A 200 -1 O ASN A 197 N SER A 153 SHEET 3 AA5 3 THR A 205 VAL A 211 -1 O VAL A 207 N VAL A 198 SHEET 1 AA6 4 MET B 4 THR B 7 0 SHEET 2 AA6 4 ALA B 19 SER B 25 -1 O ARG B 24 N THR B 5 SHEET 3 AA6 4 ASP B 70 ILE B 75 -1 O PHE B 71 N CYS B 23 SHEET 4 AA6 4 VAL B 62 SER B 67 -1 N SER B 63 O LYS B 74 SHEET 1 AA7 6 SER B 10 ARG B 14 0 SHEET 2 AA7 6 THR B 102 LYS B 107 1 O LYS B 103 N LEU B 11 SHEET 3 AA7 6 GLY B 84 GLN B 90 -1 N GLY B 84 O LEU B 104 SHEET 4 AA7 6 LEU B 33 GLN B 38 -1 N TYR B 36 O TYR B 87 SHEET 5 AA7 6 LYS B 45 TYR B 49 -1 O LEU B 47 N TRP B 35 SHEET 6 AA7 6 ASN B 53 ARG B 54 -1 O ASN B 53 N TYR B 49 SHEET 1 AA8 4 SER B 10 ARG B 14 0 SHEET 2 AA8 4 THR B 102 LYS B 107 1 O LYS B 103 N LEU B 11 SHEET 3 AA8 4 GLY B 84 GLN B 90 -1 N GLY B 84 O LEU B 104 SHEET 4 AA8 4 THR B 97 PHE B 98 -1 O THR B 97 N GLN B 90 SHEET 1 AA9 4 SER B 114 PHE B 118 0 SHEET 2 AA9 4 THR B 129 PHE B 139 -1 O LEU B 135 N PHE B 116 SHEET 3 AA9 4 TYR B 173 SER B 182 -1 O LEU B 179 N VAL B 132 SHEET 4 AA9 4 SER B 159 VAL B 163 -1 N GLN B 160 O THR B 178 SHEET 1 AB1 4 ALA B 153 LEU B 154 0 SHEET 2 AB1 4 LYS B 145 VAL B 150 -1 N VAL B 150 O ALA B 153 SHEET 3 AB1 4 VAL B 191 THR B 197 -1 O ALA B 193 N LYS B 149 SHEET 4 AB1 4 VAL B 205 ASN B 210 -1 O VAL B 205 N VAL B 196 SHEET 1 AB2 4 GLN D 3 GLN D 6 0 SHEET 2 AB2 4 VAL D 18 SER D 25 -1 O LYS D 23 N GLN D 5 SHEET 3 AB2 4 THR D 77 LEU D 82 -1 O MET D 80 N LEU D 20 SHEET 4 AB2 4 ALA D 67 ASP D 72 -1 N THR D 70 O TYR D 79 SHEET 1 AB3 6 GLU D 10 VAL D 12 0 SHEET 2 AB3 6 THR D 107 VAL D 111 1 O THR D 108 N GLU D 10 SHEET 3 AB3 6 ALA D 88 LEU D 95 -1 N ALA D 88 O VAL D 109 SHEET 4 AB3 6 GLU D 33 THR D 40 -1 N GLU D 33 O LEU D 95 SHEET 5 AB3 6 GLY D 44 ILE D 51 -1 O ILE D 48 N TRP D 36 SHEET 6 AB3 6 THR D 57 TYR D 59 -1 O ALA D 58 N ALA D 50 SHEET 1 AB4 4 SER D 120 LEU D 124 0 SHEET 2 AB4 4 THR D 135 TYR D 145 -1 O LEU D 141 N PHE D 122 SHEET 3 AB4 4 TYR D 176 PRO D 185 -1 O VAL D 184 N ALA D 136 SHEET 4 AB4 4 VAL D 163 THR D 165 -1 N HIS D 164 O VAL D 181 SHEET 1 AB5 4 THR D 131 SER D 132 0 SHEET 2 AB5 4 THR D 135 TYR D 145 -1 O THR D 135 N SER D 132 SHEET 3 AB5 4 TYR D 176 PRO D 185 -1 O VAL D 184 N ALA D 136 SHEET 4 AB5 4 VAL D 169 LEU D 170 -1 N VAL D 169 O SER D 177 SHEET 1 AB6 3 THR D 151 TRP D 154 0 SHEET 2 AB6 3 TYR D 194 HIS D 200 -1 O ASN D 197 N SER D 153 SHEET 3 AB6 3 THR D 205 VAL D 211 -1 O VAL D 207 N VAL D 198 SHEET 1 AB7 4 MET E 4 THR E 7 0 SHEET 2 AB7 4 ALA E 19 SER E 25 -1 O ARG E 24 N THR E 5 SHEET 3 AB7 4 ASP E 70 ILE E 75 -1 O PHE E 71 N CYS E 23 SHEET 4 AB7 4 VAL E 62 SER E 67 -1 N SER E 63 O LYS E 74 SHEET 1 AB8 6 SER E 10 ARG E 14 0 SHEET 2 AB8 6 THR E 102 LYS E 107 1 O LYS E 103 N LEU E 11 SHEET 3 AB8 6 GLY E 84 GLN E 90 -1 N GLY E 84 O LEU E 104 SHEET 4 AB8 6 LEU E 33 GLN E 38 -1 N GLU E 34 O PHE E 89 SHEET 5 AB8 6 LYS E 45 TYR E 49 -1 O LEU E 47 N TRP E 35 SHEET 6 AB8 6 ASN E 53 ARG E 54 -1 O ASN E 53 N TYR E 49 SHEET 1 AB9 4 SER E 10 ARG E 14 0 SHEET 2 AB9 4 THR E 102 LYS E 107 1 O LYS E 103 N LEU E 11 SHEET 3 AB9 4 GLY E 84 GLN E 90 -1 N GLY E 84 O LEU E 104 SHEET 4 AB9 4 THR E 97 PHE E 98 -1 O THR E 97 N GLN E 90 SHEET 1 AC1 4 SER E 114 PHE E 118 0 SHEET 2 AC1 4 THR E 129 PHE E 139 -1 O ASN E 137 N SER E 114 SHEET 3 AC1 4 TYR E 173 SER E 182 -1 O LEU E 179 N VAL E 132 SHEET 4 AC1 4 SER E 159 VAL E 163 -1 N GLN E 160 O THR E 178 SHEET 1 AC2 4 ALA E 153 LEU E 154 0 SHEET 2 AC2 4 LYS E 145 VAL E 150 -1 N VAL E 150 O ALA E 153 SHEET 3 AC2 4 VAL E 191 THR E 197 -1 O ALA E 193 N LYS E 149 SHEET 4 AC2 4 VAL E 205 ASN E 210 -1 O VAL E 205 N VAL E 196 SSBOND 1 CYS A 22 CYS A 92 1555 1555 2.04 SSBOND 2 CYS A 140 CYS A 196 1555 1555 2.05 SSBOND 3 CYS B 23 CYS B 88 1555 1555 2.04 SSBOND 4 CYS B 134 CYS B 194 1555 1555 2.04 SSBOND 5 CYS D 22 CYS D 92 1555 1555 2.04 SSBOND 6 CYS D 140 CYS D 196 1555 1555 2.04 SSBOND 7 CYS E 23 CYS E 88 1555 1555 2.04 SSBOND 8 CYS E 134 CYS E 194 1555 1555 2.05 CISPEP 1 PHE A 146 PRO A 147 0 -6.67 CISPEP 2 GLU A 148 PRO A 149 0 -4.43 CISPEP 3 THR B 7 PRO B 8 0 -4.60 CISPEP 4 VAL B 94 PRO B 95 0 -1.41 CISPEP 5 TYR B 140 PRO B 141 0 3.36 CISPEP 6 PHE D 146 PRO D 147 0 -7.24 CISPEP 7 GLU D 148 PRO D 149 0 -2.33 CISPEP 8 THR E 7 PRO E 8 0 -4.64 CISPEP 9 VAL E 94 PRO E 95 0 -1.87 CISPEP 10 TYR E 140 PRO E 141 0 4.70 CRYST1 79.565 61.034 88.654 90.00 91.89 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 0.012568 0.000000 0.000414 0.00000 SCALE2 0.000000 0.016384 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011286 0.00000