PDB Short entry for 2KNX HEADER PROTEIN BINDING 07-SEP-09 2KNX TITLE SOLUTION STRUCTURE OF COMPLEMENT REPEAT CR17 FROM LRP-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROLOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 2770-2817; COMPND 5 SYNONYM: LRP, ALPHA-2-MACROGLOBULIN RECEPTOR, A2MR, APOLIPOPROTEIN E COMPND 6 RECEPTOR, APOER, LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1 COMPND 7 85 KDA SUBUNIT, LRP-85, LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED COMPND 8 PROTEIN 1 515 KDA SUBUNIT, LRP-515, LOW-DENSITY LIPOPROTEIN RECEPTOR- COMPND 9 RELATED PROTEIN 1 INTRACELLULAR DOMAIN, LRPICD; COMPND 10 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: LRP1, A2MR, APR; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMMHB KEYWDS LDLR, LIGAND BINDING MODULE, LIGAND BINDING REPEAT, COMPLEMENT KEYWDS 2 REPEAT, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.GUTTMAN,E.KOMIVES REVDAT 4 14-JUN-23 2KNX 1 REMARK REVDAT 3 26-FEB-20 2KNX 1 REMARK SEQADV REVDAT 2 05-MAY-10 2KNX 1 JRNL REVDAT 1 14-APR-10 2KNX 0 JRNL AUTH M.GUTTMAN,J.H.PRIETO,T.M.HANDEL,P.J.DOMAILLE,E.A.KOMIVES JRNL TITL STRUCTURE OF THE MINIMAL INTERFACE BETWEEN APOE AND LRP. JRNL REF J.MOL.BIOL. V. 398 306 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20303980 JRNL DOI 10.1016/J.JMB.2010.03.022 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.2, ARIA 2.2, CNS 1.2 REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), LINGE, REMARK 3 O'DONOGHUE AND NILGES (ARIA), BRUNGER, ADAMS, REMARK 3 CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KNX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000101354. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 307; 298 REMARK 210 PH : 7.45; 7.45 REMARK 210 IONIC STRENGTH : 0.15; 0.15 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 150 MM SODIUM CHLORIDE, 20 MM [U REMARK 210 -99% 2H] HEPES, 0.7 MM [U-99% REMARK 210 13C; U-99% 15N] PROTEIN, 5 MM REMARK 210 CALCIUM ION, 3 MM SODIUM AZIDE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HNCO; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D HCNH REMARK 210 NOESY; 3D CBCANH; 2D 1H-15N HSQC REMARK 210 HETERNUCLEAR NOE; 2D 1H-15N HSQC REMARK 210 T1 RELAXATION; 2D 1H-15N HSQC T2 REMARK 210 RELAXATION 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 : CNS 1.2, NMRPIPE, AZARA 2.7, REMARK 210 SPARKY 3.113 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 93 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 SER A 2 73.68 60.89 REMARK 500 1 LYS A 5 -74.62 -82.16 REMARK 500 1 SER A 10 66.02 -114.19 REMARK 500 1 HIS A 18 59.18 -110.01 REMARK 500 1 LYS A 31 88.86 -57.35 REMARK 500 1 ASN A 48 -76.69 -147.05 REMARK 500 1 SER A 49 99.44 53.59 REMARK 500 2 LYS A 5 -83.74 -150.68 REMARK 500 2 THR A 6 -91.17 51.09 REMARK 500 2 CYS A 27 58.04 38.63 REMARK 500 2 LYS A 31 88.33 -61.02 REMARK 500 2 LEU A 46 65.31 69.22 REMARK 500 3 SER A 2 -74.82 -125.25 REMARK 500 3 GLU A 3 29.83 -160.66 REMARK 500 3 LYS A 5 -60.87 -102.03 REMARK 500 3 CYS A 7 69.19 -151.54 REMARK 500 3 THR A 17 163.33 179.40 REMARK 500 3 HIS A 18 40.12 -98.35 REMARK 500 3 CYS A 27 69.16 39.29 REMARK 500 3 LYS A 31 92.05 -53.14 REMARK 500 3 CYS A 33 -174.91 -65.22 REMARK 500 3 LEU A 46 -83.40 66.81 REMARK 500 3 TYR A 47 106.24 -47.03 REMARK 500 3 ASN A 48 -91.51 29.13 REMARK 500 4 SER A 2 79.79 -164.69 REMARK 500 4 CYS A 7 74.91 -151.38 REMARK 500 4 HIS A 18 54.53 -104.52 REMARK 500 4 CYS A 27 58.49 36.92 REMARK 500 4 LYS A 31 84.15 -60.12 REMARK 500 4 LEU A 46 77.06 54.80 REMARK 500 4 TYR A 47 36.42 -174.03 REMARK 500 5 GLU A 3 -43.96 -176.42 REMARK 500 5 CYS A 7 -169.04 53.92 REMARK 500 5 SER A 10 55.52 -97.28 REMARK 500 5 CYS A 27 59.36 38.03 REMARK 500 5 LYS A 31 83.15 -62.42 REMARK 500 5 LEU A 46 -59.23 -141.49 REMARK 500 5 TYR A 47 93.50 -53.47 REMARK 500 6 SER A 2 -67.51 -173.64 REMARK 500 6 GLU A 3 108.95 60.20 REMARK 500 6 LYS A 5 -76.05 66.04 REMARK 500 6 THR A 6 -85.86 51.98 REMARK 500 6 CYS A 7 69.18 -115.57 REMARK 500 6 LYS A 31 81.77 -62.38 REMARK 500 6 LEU A 46 -67.26 71.75 REMARK 500 6 SER A 49 31.55 -149.30 REMARK 500 7 SER A 2 -73.43 -114.85 REMARK 500 7 GLU A 3 -161.07 -110.44 REMARK 500 7 THR A 6 -75.02 -59.00 REMARK 500 7 CYS A 7 -67.12 -106.44 REMARK 500 REMARK 500 THIS ENTRY HAS 163 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 51 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP A 25 O REMARK 620 2 ASP A 28 OD1 54.7 REMARK 620 3 ASP A 30 O 123.7 79.9 REMARK 620 4 ASP A 32 OD2 92.0 90.9 53.7 REMARK 620 5 ASP A 38 OD1 137.4 158.6 97.1 104.4 REMARK 620 6 GLU A 39 OE2 108.0 62.1 69.4 120.7 96.9 REMARK 620 N 1 2 3 4 5 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 51 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16482 RELATED DB: BMRB DBREF 2KNX A 3 50 UNP Q07954 LRP1_HUMAN 2770 2817 SEQADV 2KNX GLY A 1 UNP Q07954 EXPRESSION TAG SEQADV 2KNX SER A 2 UNP Q07954 EXPRESSION TAG SEQRES 1 A 50 GLY SER GLU GLY LYS THR CYS GLY PRO SER SER PHE SER SEQRES 2 A 50 CYS PRO GLY THR HIS VAL CYS VAL PRO GLU ARG TRP LEU SEQRES 3 A 50 CYS ASP GLY ASP LYS ASP CYS ALA ASP GLY ALA ASP GLU SEQRES 4 A 50 SER ILE ALA ALA GLY CYS LEU TYR ASN SER THR HET CA A 51 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 GLY A 36 GLY A 44 5 9 SHEET 1 A 2 SER A 11 CYS A 14 0 SHEET 2 A 2 VAL A 19 PRO A 22 -1 O VAL A 21 N PHE A 12 SSBOND 1 CYS A 7 CYS A 20 1555 1555 2.03 SSBOND 2 CYS A 14 CYS A 33 1555 1555 2.03 SSBOND 3 CYS A 27 CYS A 45 1555 1555 2.03 LINK O TRP A 25 CA CA A 51 1555 1555 2.77 LINK OD1 ASP A 28 CA CA A 51 1555 1555 2.78 LINK O ASP A 30 CA CA A 51 1555 1555 2.77 LINK OD2 ASP A 32 CA CA A 51 1555 1555 2.78 LINK OD1 ASP A 38 CA CA A 51 1555 1555 2.78 LINK OE2 GLU A 39 CA CA A 51 1555 1555 2.79 SITE 1 AC1 7 TRP A 25 CYS A 27 ASP A 28 ASP A 30 SITE 2 AC1 7 ASP A 32 ASP A 38 GLU A 39 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