HEADER SIGNALING PROTEIN 29-JUL-22 8DVN TITLE CRYSTAL STRUCTURE OF LRP6 E3E4 IN COMPLEX WITH DISULFIDE CONSTRAINED TITLE 2 PEPTIDE E3.10 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 6; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LRP-6; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: E3.10 DISULFIDE CONSTRAINED PEPTIDE; COMPND 8 CHAIN: B; COMPND 9 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: LRP6; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_COMMON: CABBAGE LOOPER; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630 KEYWDS LRP6, E3E4, WNT SIGNALING, SIGNALING PROTEIN, DISULFIDE CONSTRAINED KEYWDS 2 PEPTIDE, WNT AGONISM EXPDTA X-RAY DIFFRACTION AUTHOR A.K.THAKUR,N.P.D.LIAU,J.SUDHAMSU,R.N.HANNOUSH REVDAT 4 15-NOV-23 8DVN 1 REMARK REVDAT 3 25-OCT-23 8DVN 1 REMARK REVDAT 2 03-MAY-23 8DVN 1 JRNL REVDAT 1 29-MAR-23 8DVN 0 JRNL AUTH A.K.THAKUR,S.E.MILLER,N.P.D.LIAU,S.HWANG,S.HANSEN, JRNL AUTH 2 F.DE SOUSA E MELO,J.SUDHAMSU,R.N.HANNOUSH JRNL TITL SYNTHETIC MULTIVALENT DISULFIDE-CONSTRAINED PEPTIDE AGONISTS JRNL TITL 2 POTENTIATE WNT1/ BETA-CATENIN SIGNALING VIA LRP6 CORECEPTOR JRNL TITL 3 CLUSTERING. JRNL REF ACS CHEM.BIOL. V. 18 772 2023 JRNL REFN ESSN 1554-8937 JRNL PMID 36893429 JRNL DOI 10.1021/ACSCHEMBIO.2C00753 REMARK 2 REMARK 2 RESOLUTION. 2.53 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC3-4406_FINAL 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.53 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 34563 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3341 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 44.3300 - 7.2800 1.00 2573 155 0.1776 0.1884 REMARK 3 2 7.2800 - 5.7800 1.00 2575 141 0.1845 0.1940 REMARK 3 3 5.7800 - 5.0500 1.00 2608 141 0.1639 0.2136 REMARK 3 4 5.0500 - 4.5900 1.00 2595 142 0.1425 0.1466 REMARK 3 5 4.5900 - 4.2600 1.00 2598 138 0.1371 0.1886 REMARK 3 6 4.2600 - 4.0100 1.00 2584 134 0.1585 0.2025 REMARK 3 7 4.0100 - 3.8100 1.00 2595 152 0.1730 0.2091 REMARK 3 8 3.8100 - 3.6400 1.00 2608 124 0.1998 0.2439 REMARK 3 9 3.6400 - 3.5000 1.00 2600 138 0.2280 0.3039 REMARK 3 10 3.5000 - 3.3800 1.00 2576 127 0.2209 0.2796 REMARK 3 11 3.3800 - 3.2800 1.00 2609 156 0.2268 0.2997 REMARK 3 12 3.2800 - 3.1800 1.00 2593 144 0.2418 0.3088 REMARK 3 13 3.1800 - 3.1000 1.00 2569 124 0.2610 0.3988 REMARK 3 14 3.1000 - 3.0200 1.00 2640 136 0.3004 0.3663 REMARK 3 15 3.0200 - 2.9600 1.00 2544 151 0.3215 0.3831 REMARK 3 16 2.9600 - 2.8900 1.00 2601 137 0.3283 0.4204 REMARK 3 17 2.8900 - 2.8300 1.00 2588 146 0.3225 0.3766 REMARK 3 18 2.8300 - 2.7800 1.00 2591 157 0.3239 0.3904 REMARK 3 19 2.7800 - 2.7300 1.00 2607 116 0.3519 0.3279 REMARK 3 20 2.7300 - 2.6900 1.00 2608 124 0.3660 0.3550 REMARK 3 21 2.6900 - 2.6400 1.00 2594 135 0.3665 0.4097 REMARK 3 22 2.6400 - 2.6000 0.99 2575 150 0.3982 0.3906 REMARK 3 23 2.6000 - 2.5600 0.99 2585 140 0.4172 0.4571 REMARK 3 24 2.5600 - 2.5300 0.98 2515 133 0.4336 0.4215 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 33.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 86.88 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 630 THROUGH 920) REMARK 3 ORIGIN FOR THE GROUP (A): 12.3790 24.5745 17.5471 REMARK 3 T TENSOR REMARK 3 T11: 0.4774 T22: 0.5712 REMARK 3 T33: 0.3737 T12: 0.0155 REMARK 3 T13: -0.0056 T23: -0.0148 REMARK 3 L TENSOR REMARK 3 L11: 2.1845 L22: 6.0029 REMARK 3 L33: 3.0319 L12: -1.2792 REMARK 3 L13: -0.7740 L23: -0.5648 REMARK 3 S TENSOR REMARK 3 S11: -0.1712 S12: -0.3154 S13: 0.1131 REMARK 3 S21: 0.7128 S22: 0.4103 S23: -0.0240 REMARK 3 S31: 0.1002 S32: 0.0126 S33: -0.2385 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 921 THROUGH 1245 ) REMARK 3 ORIGIN FOR THE GROUP (A): 34.5498 -5.8476 -7.6097 REMARK 3 T TENSOR REMARK 3 T11: 0.9966 T22: 0.5322 REMARK 3 T33: 0.5097 T12: 0.0714 REMARK 3 T13: -0.0362 T23: -0.0132 REMARK 3 L TENSOR REMARK 3 L11: 3.0448 L22: 3.5714 REMARK 3 L33: 2.4032 L12: -0.6614 REMARK 3 L13: -0.6910 L23: 0.2306 REMARK 3 S TENSOR REMARK 3 S11: -0.1028 S12: 0.0626 S13: -0.4251 REMARK 3 S21: -0.0391 S22: -0.0799 S23: -0.2244 REMARK 3 S31: 0.9511 S32: 0.1313 S33: 0.1474 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 1 THROUGH 32 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.7742 37.4973 -2.5571 REMARK 3 T TENSOR REMARK 3 T11: 0.9539 T22: 1.0118 REMARK 3 T33: 0.9098 T12: -0.0721 REMARK 3 T13: 0.1042 T23: 0.1782 REMARK 3 L TENSOR REMARK 3 L11: 3.1837 L22: 2.7704 REMARK 3 L33: 8.3456 L12: -2.4875 REMARK 3 L13: 1.8231 L23: -3.5842 REMARK 3 S TENSOR REMARK 3 S11: -0.3384 S12: 1.9817 S13: 1.2458 REMARK 3 S21: -0.5275 S22: -0.1693 S23: -0.6677 REMARK 3 S31: -1.7263 S32: 0.1494 S33: 0.5496 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 8DVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1000267447. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-20 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000030 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 34563 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.530 REMARK 200 RESOLUTION RANGE LOW (A) : 44.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.53 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHENIX REMARK 200 STARTING MODEL: 4A0P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M KSCN, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 34.04850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 63.58200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.39150 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 63.58200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.04850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.39150 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 APPLY THE FOLLOWING TO CHAINS: A, B, C, 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 PRO A 1008 REMARK 465 SER A 1009 REMARK 465 GLN A 1010 REMARK 465 ASN A 1011 REMARK 465 PRO A 1246 REMARK 465 PRO A 1247 REMARK 465 THR A 1248 REMARK 465 CYS A 1249 REMARK 465 SER A 1250 REMARK 465 PRO A 1251 REMARK 465 GLN A 1252 REMARK 465 GLN A 1253 REMARK 465 GLY A 1254 REMARK 465 ASN A 1255 REMARK 465 SER A 1256 REMARK 465 HIS A 1257 REMARK 465 HIS A 1258 REMARK 465 HIS A 1259 REMARK 465 HIS A 1260 REMARK 465 HIS A 1261 REMARK 465 HIS A 1262 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 ARG A 639 -116.10 50.81 REMARK 500 ASN A 651 109.51 -57.91 REMARK 500 ARG A 751 -60.40 -124.94 REMARK 500 GLN A 842 -120.77 53.03 REMARK 500 ARG A 853 70.40 49.11 REMARK 500 GLN A 940 -160.14 -123.04 REMARK 500 GLN A1015 76.79 -160.97 REMARK 500 ARG A1079 -7.86 75.84 REMARK 500 GLN A1146 76.53 -152.20 REMARK 500 GLU A1154 -119.66 54.68 REMARK 500 GLU A1240 15.08 57.16 REMARK 500 GLN B 15 48.02 -87.13 REMARK 500 LEU B 20 40.65 -107.73 REMARK 500 ALA B 21 15.09 59.55 REMARK 500 CYS B 25 146.45 85.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 OCS A1032 -14.25 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 A1303 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 724 O REMARK 620 2 ASN A 727 OD1 79.7 REMARK 620 3 SER A 749 OG 89.7 84.4 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 838 O REMARK 620 2 ASP A 878 OD1 104.7 REMARK 620 3 ILE A 879 O 93.3 66.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1304 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A1018 OD2 REMARK 620 2 LEU A1019 O 93.5 REMARK 620 3 ILE A1062 O 71.6 86.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1305 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A1150 O REMARK 620 2 ASP A1190 OD1 112.5 REMARK 620 3 ILE A1191 O 85.2 65.6 REMARK 620 N 1 2 DBREF 8DVN A 631 1253 UNP O75581 LRP6_HUMAN 631 1253 DBREF 8DVN B 1 32 PDB 8DVN 8DVN 1 32 SEQADV 8DVN SER A 630 UNP O75581 EXPRESSION TAG SEQADV 8DVN ILE A 1062 UNP O75581 VAL 1062 VARIANT SEQADV 8DVN GLY A 1254 UNP O75581 EXPRESSION TAG SEQADV 8DVN ASN A 1255 UNP O75581 EXPRESSION TAG SEQADV 8DVN SER A 1256 UNP O75581 EXPRESSION TAG SEQADV 8DVN HIS A 1257 UNP O75581 EXPRESSION TAG SEQADV 8DVN HIS A 1258 UNP O75581 EXPRESSION TAG SEQADV 8DVN HIS A 1259 UNP O75581 EXPRESSION TAG SEQADV 8DVN HIS A 1260 UNP O75581 EXPRESSION TAG SEQADV 8DVN HIS A 1261 UNP O75581 EXPRESSION TAG SEQADV 8DVN HIS A 1262 UNP O75581 EXPRESSION TAG SEQRES 1 A 633 SER GLU ALA PHE LEU LEU PHE SER ARG ARG ALA ASP ILE SEQRES 2 A 633 ARG ARG ILE SER LEU GLU THR ASN ASN ASN ASN VAL ALA SEQRES 3 A 633 ILE PRO LEU THR GLY VAL LYS GLU ALA SER ALA LEU ASP SEQRES 4 A 633 PHE ASP VAL THR ASP ASN ARG ILE TYR TRP THR ASP ILE SEQRES 5 A 633 SER LEU LYS THR ILE SER ARG ALA PHE MET ASN GLY SER SEQRES 6 A 633 ALA LEU GLU HIS VAL VAL GLU PHE GLY LEU ASP TYR PRO SEQRES 7 A 633 GLU GLY MET ALA VAL ASP TRP LEU GLY LYS ASN LEU TYR SEQRES 8 A 633 TRP ALA ASP THR GLY THR ASN ARG ILE GLU VAL SER LYS SEQRES 9 A 633 LEU ASP GLY GLN HIS ARG GLN VAL LEU VAL TRP LYS ASP SEQRES 10 A 633 LEU ASP SER PRO ARG ALA LEU ALA LEU ASP PRO ALA GLU SEQRES 11 A 633 GLY PHE MET TYR TRP THR GLU TRP GLY GLY LYS PRO LYS SEQRES 12 A 633 ILE ASP ARG ALA ALA MET ASP GLY SER GLU ARG THR THR SEQRES 13 A 633 LEU VAL PRO ASN VAL GLY ARG ALA ASN GLY LEU THR ILE SEQRES 14 A 633 ASP TYR ALA LYS ARG ARG LEU TYR TRP THR ASP LEU ASP SEQRES 15 A 633 THR ASN LEU ILE GLU SER SER ASN MET LEU GLY LEU ASN SEQRES 16 A 633 ARG GLU VAL ILE ALA ASP ASP LEU PRO HIS PRO PHE GLY SEQRES 17 A 633 LEU THR GLN TYR GLN ASP TYR ILE TYR TRP THR ASP TRP SEQRES 18 A 633 SER ARG ARG SER ILE GLU ARG ALA ASN LYS THR SER GLY SEQRES 19 A 633 GLN ASN ARG THR ILE ILE GLN GLY HIS LEU ASP TYR VAL SEQRES 20 A 633 MET ASP ILE LEU VAL PHE HIS SER SER ARG GLN SER GLY SEQRES 21 A 633 TRP ASN GLU CYS ALA SER SER ASN GLY HIS CYS SER HIS SEQRES 22 A 633 LEU CYS LEU ALA VAL PRO VAL GLY GLY PHE VAL CYS GLY SEQRES 23 A 633 CYS PRO ALA HIS TYR SER LEU ASN ALA ASP ASN ARG THR SEQRES 24 A 633 CYS SER ALA PRO THR THR PHE LEU LEU PHE SER GLN LYS SEQRES 25 A 633 SER ALA ILE ASN ARG MET VAL ILE ASP GLU GLN GLN SER SEQRES 26 A 633 PRO ASP ILE ILE LEU PRO ILE HIS SER LEU ARG ASN VAL SEQRES 27 A 633 ARG ALA ILE ASP TYR ASP PRO LEU ASP LYS GLN LEU TYR SEQRES 28 A 633 TRP ILE ASP SER ARG GLN ASN MET ILE ARG LYS ALA GLN SEQRES 29 A 633 GLU ASP GLY SER GLN GLY PHE THR VAL VAL VAL SER SER SEQRES 30 A 633 VAL PRO SER GLN ASN LEU GLU ILE GLN PRO TYR ASP LEU SEQRES 31 A 633 SER ILE ASP ILE TYR SER ARG TYR ILE TYR TRP THR OCS SEQRES 32 A 633 GLU ALA THR ASN VAL ILE ASN VAL THR ARG LEU ASP GLY SEQRES 33 A 633 ARG SER VAL GLY VAL VAL LEU LYS GLY GLU GLN ASP ARG SEQRES 34 A 633 PRO ARG ALA ILE VAL VAL ASN PRO GLU LYS GLY TYR MET SEQRES 35 A 633 TYR PHE THR ASN LEU GLN GLU ARG SER PRO LYS ILE GLU SEQRES 36 A 633 ARG ALA ALA LEU ASP GLY THR GLU ARG GLU VAL LEU PHE SEQRES 37 A 633 PHE SER GLY LEU SER LYS PRO ILE ALA LEU ALA LEU ASP SEQRES 38 A 633 SER ARG LEU GLY LYS LEU PHE TRP ALA ASP SER ASP LEU SEQRES 39 A 633 ARG ARG ILE GLU SER SER ASP LEU SER GLY ALA ASN ARG SEQRES 40 A 633 ILE VAL LEU GLU ASP SER ASN ILE LEU GLN PRO VAL GLY SEQRES 41 A 633 LEU THR VAL PHE GLU ASN TRP LEU TYR TRP ILE ASP LYS SEQRES 42 A 633 GLN GLN GLN MET ILE GLU LYS ILE ASP MET THR GLY ARG SEQRES 43 A 633 GLU GLY ARG THR LYS VAL GLN ALA ARG ILE ALA GLN LEU SEQRES 44 A 633 SER ASP ILE HIS ALA VAL LYS GLU LEU ASN LEU GLN GLU SEQRES 45 A 633 TYR ARG GLN HIS PRO CYS ALA GLN ASP ASN GLY GLY CYS SEQRES 46 A 633 SER HIS ILE CYS LEU VAL LYS GLY ASP GLY THR THR ARG SEQRES 47 A 633 CYS SER CYS PRO MET HIS LEU VAL LEU LEU GLN ASP GLU SEQRES 48 A 633 LEU SER CYS GLY GLU PRO PRO THR CYS SER PRO GLN GLN SEQRES 49 A 633 GLY ASN SER HIS HIS HIS HIS HIS HIS SEQRES 1 B 32 GLY CYS ARG GLY LEU LYS ARG LEU TYR GLU ALA PHE CYS SEQRES 2 B 32 LYS GLN ASP SER ASP CYS LEU ALA GLY CYS VAL CYS PRO SEQRES 3 B 32 MET PHE SER GLU CYS GLY MODRES 8DVN OCS A 1032 CYS MODIFIED RESIDUE HET OCS A1032 9 HET NAG C 1 14 HET NAG C 2 14 HET BMA C 3 11 HET NAG D 1 14 HET NAG D 2 14 HET FUC D 3 10 HET NAG E 1 14 HET NAG E 2 14 HET NAG F 1 14 HET NAG F 2 14 HET NAG A1301 14 HET CA A1302 1 HET CA A1303 1 HET CA A1304 1 HET CA A1305 1 HETNAM OCS CYSTEINESULFONIC ACID HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM CA CALCIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN BMA BETA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 1 OCS C3 H7 N O5 S FORMUL 3 NAG 9(C8 H15 N O6) FORMUL 3 BMA C6 H12 O6 FORMUL 4 FUC C6 H12 O5 FORMUL 8 CA 4(CA 2+) FORMUL 12 HOH *9(H2 O) HELIX 1 AA1 HIS A 883 GLN A 887 5 5 HELIX 2 AA2 ASN A 891 CYS A 900 5 10 HELIX 3 AA3 ASN A 1198 GLN A 1204 1 7 HELIX 4 AA4 GLN A 1209 CYS A 1214 5 6 HELIX 5 AA5 CYS B 2 CYS B 13 1 12 SHEET 1 AA1 4 ASN A 653 ALA A 655 0 SHEET 2 AA1 4 ASP A 641 SER A 646 -1 N ARG A 644 O VAL A 654 SHEET 3 AA1 4 PHE A 633 ARG A 638 -1 N LEU A 634 O ILE A 645 SHEET 4 AA1 4 VAL A 876 PHE A 882 -1 O PHE A 882 N PHE A 633 SHEET 1 AA2 4 ALA A 664 ASP A 670 0 SHEET 2 AA2 4 ARG A 675 ASP A 680 -1 O ARG A 675 N ASP A 670 SHEET 3 AA2 4 THR A 685 PHE A 690 -1 O ALA A 689 N ILE A 676 SHEET 4 AA2 4 GLU A 697 VAL A 700 -1 O GLU A 697 N ARG A 688 SHEET 1 AA3 4 GLY A 709 ASP A 713 0 SHEET 2 AA3 4 ASN A 718 ASP A 723 -1 O ASN A 718 N ASP A 713 SHEET 3 AA3 4 ARG A 728 LYS A 733 -1 O SER A 732 N LEU A 719 SHEET 4 AA3 4 GLN A 740 VAL A 743 -1 O GLN A 740 N VAL A 731 SHEET 1 AA4 4 PRO A 750 LEU A 755 0 SHEET 2 AA4 4 PHE A 761 GLU A 766 -1 O THR A 765 N ARG A 751 SHEET 3 AA4 4 LYS A 772 ALA A 777 -1 O LYS A 772 N GLU A 766 SHEET 4 AA4 4 THR A 784 VAL A 787 -1 O THR A 784 N ARG A 775 SHEET 1 AA5 4 ALA A 793 ASP A 799 0 SHEET 2 AA5 4 ARG A 804 ASP A 809 -1 O ARG A 804 N ASP A 799 SHEET 3 AA5 4 LEU A 814 ASN A 819 -1 O SER A 818 N LEU A 805 SHEET 4 AA5 4 GLU A 826 ALA A 829 -1 O GLU A 826 N SER A 817 SHEET 1 AA6 4 PRO A 835 TYR A 841 0 SHEET 2 AA6 4 TYR A 844 ASP A 849 -1 O THR A 848 N PHE A 836 SHEET 3 AA6 4 SER A 854 ASN A 859 -1 O GLU A 856 N TRP A 847 SHEET 4 AA6 4 THR A 867 GLY A 871 -1 O ILE A 869 N ILE A 855 SHEET 1 AA7 2 LEU A 903 VAL A 907 0 SHEET 2 AA7 2 GLY A 911 GLY A 915 -1 O GLY A 915 N LEU A 903 SHEET 1 AA8 2 SER A 921 LEU A 922 0 SHEET 2 AA8 2 CYS A 929 SER A 930 -1 O SER A 930 N SER A 921 SHEET 1 AA9 4 ILE A 957 ILE A 958 0 SHEET 2 AA9 4 ILE A 944 MET A 947 -1 N ARG A 946 O ILE A 957 SHEET 3 AA9 4 PHE A 935 SER A 939 -1 N PHE A 938 O ASN A 945 SHEET 4 AA9 4 ASP A1190 VAL A1194 -1 O HIS A1192 N LEU A 937 SHEET 1 AB1 4 ASP A 971 ASP A 973 0 SHEET 2 AB1 4 GLN A 978 ASP A 983 -1 O TYR A 980 N ASP A 971 SHEET 3 AB1 4 MET A 988 ALA A 992 -1 O MET A 988 N ASP A 983 SHEET 4 AB1 4 PHE A1000 VAL A1003 -1 O PHE A1000 N LYS A 991 SHEET 1 AB2 4 PRO A1016 ASP A1022 0 SHEET 2 AB2 4 TYR A1027 OCS A1032 -1 O TYR A1029 N SER A1020 SHEET 3 AB2 4 VAL A1037 ARG A1042 -1 O THR A1041 N ILE A1028 SHEET 4 AB2 4 SER A1047 LYS A1053 -1 O VAL A1048 N VAL A1040 SHEET 1 AB3 4 PRO A1059 ASN A1065 0 SHEET 2 AB3 4 TYR A1070 GLN A1077 -1 O TYR A1070 N ASN A1065 SHEET 3 AB3 4 SER A1080 ALA A1087 -1 O LYS A1082 N ASN A1075 SHEET 4 AB3 4 GLU A1094 PHE A1097 -1 O LEU A1096 N ILE A1083 SHEET 1 AB4 4 PRO A1104 ASP A1110 0 SHEET 2 AB4 4 LYS A1115 ASP A1120 -1 O PHE A1117 N ALA A1108 SHEET 3 AB4 4 ARG A1125 ASP A1130 -1 O SER A1129 N LEU A1116 SHEET 4 AB4 4 ILE A1137 GLU A1140 -1 O GLU A1140 N ILE A1126 SHEET 1 AB5 4 PRO A1147 PHE A1153 0 SHEET 2 AB5 4 TRP A1156 ASP A1161 -1 O TYR A1158 N THR A1151 SHEET 3 AB5 4 MET A1166 ASP A1171 -1 O MET A1166 N ASP A1161 SHEET 4 AB5 4 THR A1179 GLN A1182 -1 O VAL A1181 N ILE A1167 SHEET 1 AB6 2 ILE A1217 LYS A1221 0 SHEET 2 AB6 2 THR A1225 SER A1229 -1 O SER A1229 N ILE A1217 SHEET 1 AB7 2 VAL A1235 LEU A1236 0 SHEET 2 AB7 2 CYS A1243 GLY A1244 -1 O GLY A1244 N VAL A1235 SSBOND 1 CYS A 893 CYS A 904 1555 1555 2.05 SSBOND 2 CYS A 900 CYS A 914 1555 1555 2.03 SSBOND 3 CYS A 916 CYS A 929 1555 1555 2.04 SSBOND 4 CYS A 1207 CYS A 1218 1555 1555 2.04 SSBOND 5 CYS A 1214 CYS A 1228 1555 1555 2.03 SSBOND 6 CYS A 1230 CYS A 1243 1555 1555 2.03 SSBOND 7 CYS B 2 CYS B 31 1555 1555 2.03 SSBOND 8 CYS B 13 CYS B 25 1555 1555 2.02 SSBOND 9 CYS B 19 CYS B 23 1555 1555 2.03 LINK ND2 ASN A 692 C1 NAG D 1 1555 1555 1.42 LINK ND2 ASN A 859 C1 NAG F 1 1555 1555 1.43 LINK ND2 ASN A 865 C1 NAG A1301 1555 1555 1.43 LINK ND2 ASN A 926 C1 NAG E 1 1555 1555 1.43 LINK C THR A1031 N OCS A1032 1555 1555 1.32 LINK C OCS A1032 N GLU A1033 1555 1555 1.34 LINK ND2 ASN A1039 C1 NAG C 1 1555 1555 1.42 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.43 LINK O4 NAG C 2 C1 BMA C 3 1555 1555 1.44 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O6 NAG D 1 C1 FUC D 3 1555 1555 1.43 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.45 LINK O6 NAG F 1 C1 NAG F 2 1555 1555 1.43 LINK O THR A 724 CA CA A1303 1555 1555 2.75 LINK OD1 ASN A 727 CA CA A1303 1555 1555 2.79 LINK OG SER A 749 CA CA A1303 1555 1555 2.83 LINK O LEU A 838 CA CA A1302 1555 1555 2.63 LINK OD1 ASP A 878 CA CA A1302 1555 1555 3.05 LINK O ILE A 879 CA CA A1302 1555 1555 2.57 LINK OD2 ASP A1018 CA CA A1304 1555 1555 2.83 LINK O LEU A1019 CA CA A1304 1555 1555 3.07 LINK O ILE A1062 CA CA A1304 1555 1555 2.62 LINK O LEU A1150 CA CA A1305 1555 1555 3.01 LINK OD1 ASP A1190 CA CA A1305 1555 1555 2.96 LINK O ILE A1191 CA CA A1305 1555 1555 2.59 CISPEP 1 PRO A 908 VAL A 909 0 -5.01 CRYST1 68.097 116.783 127.164 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 0.014685 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007864 0.00000