HEADER PROTEIN BINDING 01-AUG-11 2LGP TITLE SOLUTION STRUCTURE OF LA45 FROM LDLR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LDL-RECEPTOR CLASS A 4 AND A5 DOMAIN RESIDUES 144-235; COMPND 5 SYNONYM: LDL RECEPTOR; COMPND 6 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: LDLR; SOURCE 6 EXPRESSION_SYSTEM: CELL-FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET KEYWDS COMPLEMENT REPEAT, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.GUTTMAN,E.A.KOMIVES REVDAT 3 14-JUN-23 2LGP 1 REMARK SEQADV LINK REVDAT 2 04-JAN-12 2LGP 1 JRNL REVDAT 1 30-NOV-11 2LGP 0 JRNL AUTH M.GUTTMAN,E.A.KOMIVES JRNL TITL THE STRUCTURE, DYNAMICS, AND BINDING OF THE LA45 MODULE PAIR JRNL TITL 2 OF THE LOW-DENSITY LIPOPROTEIN RECEPTOR SUGGEST AN IMPORTANT JRNL TITL 3 ROLE FOR LA4 IN LIGAND RELEASE. JRNL REF BIOCHEMISTRY V. 50 11001 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 22091758 JRNL DOI 10.1021/BI2014486 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AZARA, ARIA 2, CNSSOLVE 2, X-PLOR NIH REMARK 3 AUTHORS : BOUCHER (AZARA), LINGE, O'DONOGHUE AND NILGES REMARK 3 (ARIA), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNSSOLVE), SCHWIETERS, KUSZEWSKI, TJANDRA REMARK 3 AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LGP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000102371. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 306 REMARK 210 PH : 7.45 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN, 5 MM CALCIUM ION, 0.02 % REMARK 210 SODIUM AZIDE, 20 MM [U-99% 2H] REMARK 210 HEPES, 150 MM SODIUM CHLORIDE, REMARK 210 90% H2O/10% D2O; 0.8 MM [U-99% REMARK 210 13C; U-99% 15N] PROTEIN, 5 MM REMARK 210 CALCIUM ION, 0.02 % SODIUM AZIDE, REMARK 210 150 MM SODIUM CHLORIDE, 20 MM REMARK 210 [U-99% 2H] HEPES, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC REMARK 210 ALIPHATIC; 2D 1H-13C HSQC REMARK 210 AROMATIC; 3D CBCA(CO)NH; 3D HNCO; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C REMARK 210 NOESY; 2D 1H-1H COSY; 2D 1H-1H REMARK 210 NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA 2, CNSSOLVE 2, X-PLOR NIH, REMARK 210 SPARKY REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 VAL A 124 60.72 -156.51 REMARK 500 1 LEU A 125 -65.07 68.40 REMARK 500 1 THR A 126 -177.33 51.26 REMARK 500 1 CYS A 127 160.22 -46.34 REMARK 500 1 SER A 137 42.67 71.85 REMARK 500 1 LEU A 143 -77.47 -67.14 REMARK 500 1 TRP A 144 -26.22 -38.35 REMARK 500 1 ALA A 145 67.97 -60.54 REMARK 500 1 CYS A 146 59.23 91.03 REMARK 500 1 ASN A 148 -37.59 174.65 REMARK 500 1 CYS A 152 -174.54 -54.54 REMARK 500 1 SER A 156 -31.66 -36.19 REMARK 500 1 TRP A 159 139.19 -32.36 REMARK 500 1 CYS A 163 -51.77 -159.74 REMARK 500 1 PHE A 169 -179.41 58.97 REMARK 500 1 GLN A 170 -68.43 68.44 REMARK 500 1 SER A 173 -172.87 64.42 REMARK 500 1 PRO A 175 30.53 -88.23 REMARK 500 1 PHE A 179 31.27 -97.12 REMARK 500 1 LEU A 184 -32.67 -39.83 REMARK 500 1 LYS A 204 32.76 70.36 REMARK 500 1 GLU A 208 -71.53 -69.50 REMARK 500 2 VAL A 124 57.89 -152.11 REMARK 500 2 LEU A 125 -62.64 68.89 REMARK 500 2 THR A 126 -98.97 52.43 REMARK 500 2 PRO A 129 -74.25 -55.15 REMARK 500 2 SER A 137 39.65 78.44 REMARK 500 2 LEU A 143 -76.90 -66.81 REMARK 500 2 TRP A 144 -31.15 -36.53 REMARK 500 2 CYS A 146 65.81 36.42 REMARK 500 2 ASN A 148 -26.31 170.07 REMARK 500 2 CYS A 152 -172.79 -55.61 REMARK 500 2 SER A 156 -34.79 -30.07 REMARK 500 2 TRP A 159 139.03 -31.26 REMARK 500 2 ARG A 162 53.30 -90.86 REMARK 500 2 CYS A 163 -46.44 -159.96 REMARK 500 2 TYR A 167 31.27 -99.08 REMARK 500 2 VAL A 168 -77.27 66.76 REMARK 500 2 PHE A 169 -34.62 169.44 REMARK 500 2 SER A 173 160.22 61.18 REMARK 500 2 PHE A 179 30.11 -97.08 REMARK 500 2 LEU A 184 -37.96 -39.04 REMARK 500 2 VAL A 212 174.88 -58.53 REMARK 500 2 ALA A 213 86.32 -150.53 REMARK 500 3 VAL A 124 56.14 -155.89 REMARK 500 3 LEU A 125 -61.69 69.18 REMARK 500 3 THR A 126 -99.91 52.79 REMARK 500 3 PRO A 129 -73.79 -55.92 REMARK 500 3 SER A 137 38.82 79.05 REMARK 500 3 LEU A 143 -77.17 -67.12 REMARK 500 REMARK 500 THIS ENTRY HAS 428 RAMACHANDRAN OUTLIERS. 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 A 215 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 144 O REMARK 620 2 ASP A 147 OD1 92.1 REMARK 620 3 ASP A 147 OD2 83.4 15.1 REMARK 620 4 ASP A 149 O 130.3 65.4 80.3 REMARK 620 5 ASP A 151 OD2 133.6 94.3 91.4 93.6 REMARK 620 6 ASP A 151 OD1 162.4 82.6 87.6 62.3 31.3 REMARK 620 7 ASP A 157 OD2 88.1 119.3 131.0 69.1 126.8 109.1 REMARK 620 8 GLU A 158 OE2 72.1 68.5 77.5 58.6 151.2 120.6 54.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 216 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 193 O REMARK 620 2 ASP A 196 OD1 87.1 REMARK 620 3 ASP A 196 OD2 65.1 23.6 REMARK 620 4 GLY A 198 O 129.7 59.2 81.8 REMARK 620 5 ASP A 200 OD1 125.8 73.0 81.6 81.7 REMARK 620 6 ASP A 206 OD2 78.4 121.1 120.1 88.1 154.5 REMARK 620 7 GLU A 207 OE2 79.0 66.8 72.6 54.7 131.3 54.4 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 216 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16480 RELATED DB: BMRB DBREF 2LGP A 123 214 UNP P01130 LDLR_HUMAN 144 235 SEQADV 2LGP GLY A 121 UNP P01130 EXPRESSION TAG SEQADV 2LGP SER A 122 UNP P01130 EXPRESSION TAG SEQRES 1 A 94 GLY SER PRO VAL LEU THR CYS GLY PRO ALA SER PHE GLN SEQRES 2 A 94 CYS ASN SER SER THR CYS ILE PRO GLN LEU TRP ALA CYS SEQRES 3 A 94 ASP ASN ASP PRO ASP CYS GLU ASP GLY SER ASP GLU TRP SEQRES 4 A 94 PRO GLN ARG CYS ARG GLY LEU TYR VAL PHE GLN GLY ASP SEQRES 5 A 94 SER SER PRO CYS SER ALA PHE GLU PHE HIS CYS LEU SER SEQRES 6 A 94 GLY GLU CYS ILE HIS SER SER TRP ARG CYS ASP GLY GLY SEQRES 7 A 94 PRO ASP CYS LYS ASP LYS SER ASP GLU GLU ASN CYS ALA SEQRES 8 A 94 VAL ALA THR HET CA A 215 1 HET CA A 216 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 SER A 192 ARG A 194 5 3 HELIX 2 2 LYS A 204 ALA A 211 1 8 SHEET 1 A 2 PHE A 132 CYS A 134 0 SHEET 2 A 2 THR A 138 ILE A 140 -1 O ILE A 140 N PHE A 132 SHEET 1 B 2 GLU A 180 CYS A 183 0 SHEET 2 B 2 GLU A 187 HIS A 190 -1 O ILE A 189 N PHE A 181 SSBOND 1 CYS A 127 CYS A 139 1555 1555 2.03 SSBOND 2 CYS A 134 CYS A 152 1555 1555 2.03 SSBOND 3 CYS A 146 CYS A 163 1555 1555 2.03 SSBOND 4 CYS A 176 CYS A 188 1555 1555 2.03 SSBOND 5 CYS A 183 CYS A 201 1555 1555 2.03 SSBOND 6 CYS A 195 CYS A 210 1555 1555 2.03 LINK O TRP A 144 CA CA A 215 1555 1555 2.63 LINK OD1 ASP A 147 CA CA A 215 1555 1555 4.66 LINK OD2 ASP A 147 CA CA A 215 1555 1555 2.66 LINK O ASP A 149 CA CA A 215 1555 1555 2.71 LINK OD2 ASP A 151 CA CA A 215 1555 1555 3.99 LINK OD1 ASP A 151 CA CA A 215 1555 1555 2.69 LINK OD2 ASP A 157 CA CA A 215 1555 1555 2.67 LINK OE2 GLU A 158 CA CA A 215 1555 1555 2.78 LINK O TRP A 193 CA CA A 216 1555 1555 2.66 LINK OD1 ASP A 196 CA CA A 216 1555 1555 4.40 LINK OD2 ASP A 196 CA CA A 216 1555 1555 2.72 LINK O GLY A 198 CA CA A 216 1555 1555 2.66 LINK OD1 ASP A 200 CA CA A 216 1555 1555 2.68 LINK OD2 ASP A 206 CA CA A 216 1555 1555 2.66 LINK OE2 GLU A 207 CA CA A 216 1555 1555 2.75 SITE 1 AC1 6 TRP A 144 ASP A 147 ASP A 149 ASP A 151 SITE 2 AC1 6 ASP A 157 GLU A 158 SITE 1 AC2 6 TRP A 193 ASP A 196 GLY A 198 ASP A 200 SITE 2 AC2 6 ASP A 206 GLU A 207 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1