10 20 30 40 50 60 70 80 1F8Z - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER LIPID BINDING PROTEIN 05-JUL-00 1F8Z
TITLE NMR STRUCTURE OF THE SIXTH LIGAND-BINDING MODULE OF THE LDL TITLE 2 RECEPTOR
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SIXTH LIGAND-BINDING MODULE; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: PEPTIDE SYNTHESIS - BASED ON THE HUMAN SOURCE 4 SEQUENCE
KEYWDS LDL RECEPTOR, LIGAND-BINDING DOMAIN, CALCIUM-BINDING, KEYWDS 2 FAMILIAL HYPERCHOLESTEROLEMIA, LIPID BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR D.J.CLAYTON,I.M.BRERETON,P.A.KROON,R.SMITH
REVDAT 3 24-FEB-09 1F8Z 1 VERSN REVDAT 2 01-APR-03 1F8Z 1 JRNL REVDAT 1 18-OCT-00 1F8Z 0
JRNL AUTH D.CLAYTON,I.M.BRERETON,P.A.KROON,R.SMITH JRNL TITL THREE-DIMENSIONAL NMR STRUCTURE OF THE SIXTH JRNL TITL 2 LIGAND-BINDING MODULE OF THE HUMAN LDL RECEPTOR: JRNL TITL 3 COMPARISON OF TWO ADJACENT MODULES WITH DIFFERENT JRNL TITL 4 LIGAND BINDING SPECIFICITIES. JRNL REF FEBS LETT. V. 479 118 2000 JRNL REFN ISSN 0014-5793 JRNL PMID 10981718 JRNL DOI 10.1016/S0014-5793(00)01842-1
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : AXEL BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON 552 DISTANCE REMARK 3 CONSTRAINTS, 18 BACKBONE ANGLE RESTRAINTS AND 14 SIDECHAIN REMARK 3 ANGLE RESTRAINTS
REMARK 4 REMARK 4 1F8Z COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JUL-00. REMARK 100 THE RCSB ID CODE IS RCSB011390.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.50 REMARK 210 IONIC STRENGTH : 10 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 3 MM LB6, 10 MM CACL2, 1 MM REMARK 210 3,3,3-TRIMETHYLSILYLPROPIONATE; 3 MM LB6, 10 MM CACL2, 1 MM 3, REMARK 210 3,3-TRIMETHYLSILYLPROPIONATE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY, DQF-COSY, E-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR, AURELIA, XEASY, REMARK 210 DYANA 1.5, X-PLOR 3.1 REMARK 210 METHOD USED : STRUCTURE DETERMINATION BY REMARK 210 TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, REMARK 210 STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 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 1 CYS A 15 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 1 CYS A 22 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 2 CYS A 22 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 3 CYS A 15 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 3 CYS A 22 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 4 CYS A 22 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 6 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 7 CYS A 22 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 8 CYS A 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 9 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 11 CYS A 22 CA - CB - SG ANGL. DEV. = 7.5 DEGREES REMARK 500 12 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 13 CYS A 15 CA - CB - SG ANGL. DEV. = 7.0 DEGREES REMARK 500 13 CYS A 22 CA - CB - SG ANGL. DEV. = 6.9 DEGREES REMARK 500 14 CYS A 22 CA - CB - SG ANGL. DEV. = 7.8 DEGREES REMARK 500 15 CYS A 15 CA - CB - SG ANGL. DEV. = 7.2 DEGREES REMARK 500 15 CYS A 22 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 16 CYS A 22 CA - CB - SG ANGL. DEV. = 7.4 DEGREES REMARK 500 17 CYS A 22 CA - CB - SG ANGL. DEV. = 8.3 DEGREES REMARK 500 18 CYS A 22 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 19 CYS A 15 CA - CB - SG ANGL. DEV. = 6.7 DEGREES REMARK 500 19 CYS A 22 CA - CB - SG ANGL. DEV. = 7.3 DEGREES REMARK 500 20 CYS A 22 CA - CB - SG ANGL. DEV. = 7.7 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 1 ASP A 23 3.39 -150.33 REMARK 500 1 GLU A 25 38.03 -92.60 REMARK 500 1 TYR A 26 75.85 -2.20 REMARK 500 1 MET A 31 17.15 56.81 REMARK 500 2 CYS A 22 63.86 68.06 REMARK 500 2 ASP A 23 9.97 -150.42 REMARK 500 2 ARG A 24 28.23 43.10 REMARK 500 2 GLU A 25 41.38 -101.65 REMARK 500 2 TYR A 26 80.39 1.07 REMARK 500 2 MET A 31 17.41 55.80 REMARK 500 3 ASP A 23 3.64 -150.61 REMARK 500 3 GLU A 25 39.82 -93.95 REMARK 500 3 TYR A 26 79.06 -3.96 REMARK 500 3 MET A 31 11.17 51.23 REMARK 500 4 ASP A 23 -5.07 -141.70 REMARK 500 4 GLU A 25 44.71 -98.48 REMARK 500 4 TYR A 26 82.95 -2.60 REMARK 500 4 MET A 31 16.46 46.11 REMARK 500 5 CYS A 22 65.00 67.67 REMARK 500 5 ASP A 23 1.11 -150.48 REMARK 500 5 GLU A 25 40.48 -89.99 REMARK 500 5 TYR A 26 76.31 1.40 REMARK 500 5 MET A 31 12.54 57.51 REMARK 500 5 VAL A 38 46.80 -102.93 REMARK 500 6 ASP A 23 2.49 -150.18 REMARK 500 6 GLU A 25 43.65 -98.37 REMARK 500 6 TYR A 26 83.97 -3.66 REMARK 500 6 MET A 31 14.48 53.72 REMARK 500 6 CYS A 37 -75.50 -52.57 REMARK 500 7 ASP A 23 6.44 -150.45 REMARK 500 7 ARG A 24 29.96 48.95 REMARK 500 7 GLU A 25 41.92 -92.29 REMARK 500 7 TYR A 26 79.79 -5.74 REMARK 500 7 MET A 31 15.90 59.42 REMARK 500 8 ASP A 23 6.64 -150.60 REMARK 500 8 GLU A 25 41.76 -92.12 REMARK 500 8 TYR A 26 76.96 -6.52 REMARK 500 8 MET A 31 13.40 54.65 REMARK 500 8 VAL A 38 43.16 -95.19 REMARK 500 9 ASP A 23 9.32 -150.43 REMARK 500 9 GLU A 25 45.38 -97.83 REMARK 500 9 TYR A 26 85.73 -11.39 REMARK 500 9 MET A 31 15.65 52.17 REMARK 500 10 ASP A 23 12.17 -150.56 REMARK 500 10 ARG A 24 33.62 39.90 REMARK 500 10 GLU A 25 40.15 -96.73 REMARK 500 10 TYR A 26 76.82 1.36 REMARK 500 10 CYS A 37 -73.42 -68.87 REMARK 500 11 CYS A 22 61.59 63.48 REMARK 500 11 ASP A 23 -0.20 -143.53 REMARK 500 11 ARG A 24 26.95 45.09 REMARK 500 11 GLU A 25 46.36 -100.53 REMARK 500 11 TYR A 26 76.68 4.29 REMARK 500 11 MET A 31 13.17 58.40 REMARK 500 12 ASP A 23 3.58 -150.64 REMARK 500 12 GLU A 25 39.62 -92.16 REMARK 500 12 TYR A 26 76.68 -2.35 REMARK 500 12 MET A 31 16.26 54.76 REMARK 500 13 ASP A 23 6.45 -150.37 REMARK 500 13 GLU A 25 40.16 -94.34 REMARK 500 13 TYR A 26 77.92 -3.44 REMARK 500 13 MET A 31 13.28 57.21 REMARK 500 14 CYS A 22 60.04 65.18 REMARK 500 14 ASP A 23 8.03 -150.28 REMARK 500 14 ARG A 24 29.93 44.39 REMARK 500 14 GLU A 25 42.91 -94.76 REMARK 500 14 TYR A 26 78.90 -2.94 REMARK 500 14 MET A 31 13.62 55.99 REMARK 500 15 CYS A 22 60.85 67.70 REMARK 500 15 ASP A 23 -5.38 -142.34 REMARK 500 15 GLU A 25 41.58 -99.93 REMARK 500 15 TYR A 26 70.78 9.76 REMARK 500 15 CYS A 37 -74.32 -77.36 REMARK 500 15 VAL A 38 45.94 -101.35 REMARK 500 16 ASP A 23 2.85 -150.52 REMARK 500 16 GLU A 25 42.76 -94.19 REMARK 500 16 TYR A 26 82.72 -6.25 REMARK 500 16 MET A 31 13.45 51.23 REMARK 500 17 CYS A 22 60.08 65.39 REMARK 500 17 ASP A 23 -4.39 -147.49 REMARK 500 17 GLU A 25 36.00 -96.77 REMARK 500 17 TYR A 26 73.87 5.84 REMARK 500 17 MET A 31 14.72 59.13 REMARK 500 17 CYS A 37 -71.94 -59.53 REMARK 500 17 VAL A 38 43.35 -96.40 REMARK 500 18 ASP A 23 5.47 -150.39 REMARK 500 18 GLU A 25 41.45 -93.98 REMARK 500 18 TYR A 26 77.35 -5.40 REMARK 500 18 MET A 31 15.89 55.44 REMARK 500 19 ASP A 23 4.65 -150.36 REMARK 500 19 GLU A 25 39.35 -93.93 REMARK 500 19 TYR A 26 76.89 0.35 REMARK 500 19 MET A 31 14.36 56.49 REMARK 500 20 GLU A 25 44.69 -98.49 REMARK 500 20 TYR A 26 80.12 -11.66 REMARK 500 20 MET A 31 6.67 57.42 REMARK 500 20 CYS A 37 -70.49 -69.01 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 1 CA A 40 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ARG A 20 O REMARK 620 2 ASP A 33 OD2 87.2 REMARK 620 3 TYR A 26 N 179.5 93.3 REMARK 620 4 ASP A 27 OD2 62.9 65.0 117.3 REMARK 620 5 GLU A 25 O 138.9 101.2 41.0 84.2 REMARK 620 6 GLU A 34 OE2 70.2 82.1 109.8 122.7 150.4 REMARK 620 7 ASP A 23 OD1 61.5 140.9 118.0 113.1 117.7 66.2 REMARK 620 8 GLU A 25 N 129.9 134.6 49.7 148.8 69.3 87.3 68.5 REMARK 620 N 1 2 3 4 5 6 7
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 40
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LDL RELATED DB: PDB REMARK 900 1LDL CONTAINS THE FIRST LIGAND-BINDING MODULE OF THE LDL REMARK 900 RECEPTOR REMARK 900 RELATED ID: 1LDR RELATED DB: PDB REMARK 900 1LDR CONTAINS THE SECOND LIGAND-BINDING MODULE OF THE LDL REMARK 900 RECEPTOR
DBREF 1F8Z A 1 39 UNP P01130 LDLR_HUMAN 234 272
SEQRES 1 A 39 ALA THR CYS ARG PRO ASP GLU PHE GLN CYS SER ASP GLY SEQRES 2 A 39 ASN CYS ILE HIS GLY SER ARG GLN CYS ASP ARG GLU TYR SEQRES 3 A 39 ASP CYS LYS ASP MET SER ASP GLU VAL GLY CYS VAL ASN
HET CA A 40 1
HETNAM CA CALCIUM ION
FORMUL 2 CA CA 2+
HELIX 1 1 MET A 31 VAL A 35 5 5
SHEET 1 A 2 GLU A 7 GLN A 9 0 SHEET 2 A 2 CYS A 15 HIS A 17 -1 O ILE A 16 N PHE A 8
SSBOND 1 CYS A 3 CYS A 15 1555 1555 2.02 SSBOND 2 CYS A 10 CYS A 28 1555 1555 2.02 SSBOND 3 CYS A 22 CYS A 37 1555 1555 2.02
LINK CA CA A 40 O ARG A 20 1555 1555 2.79 LINK CA CA A 40 OD2 ASP A 33 1555 1555 2.63 LINK CA CA A 40 N TYR A 26 1555 1555 3.25 LINK CA CA A 40 OD2 ASP A 27 1555 1555 2.64 LINK CA CA A 40 O GLU A 25 1555 1555 3.19 LINK CA CA A 40 OE2 GLU A 34 1555 1555 2.62 LINK CA CA A 40 OD1 ASP A 23 1555 1555 2.65 LINK CA CA A 40 N GLU A 25 1555 1555 3.02
SITE 1 AC1 7 ARG A 20 ASP A 23 GLU A 25 TYR A 26 SITE 2 AC1 7 ASP A 27 ASP A 33 GLU A 34
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