PDB Short entry for 2FYL HEADER SURFACE ACTIVE PROTEIN 08-FEB-06 2FYL TITLE HADDOCK MODEL OF THE COMPLEX BETWEEN DOUBLE MODULE OF LRP, CR56, AND TITLE 2 FIRST DOMAIN OF RECEPTOR ASSOCIATED PROTEIN, RAP-D1. CAVEAT 2FYL CHIRALITY ERROR AT THE CB CENTER OF CYS B 65 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-2-MACROGLOBULIN RECEPTOR-ASSOCIATED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RAPD1; COMPND 5 SYNONYM: ALPHA-2- MRAP, LOW DENSITY LIPOPROTEIN RECEPTOR-RELATED COMPND 6 PROTEIN-ASSOCIATED PROTEIN 1, RAP; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: LOW-DENSITY LIPOPROTEIN RECEPTOR-RELATED PROTEIN 1; COMPND 10 CHAIN: B; COMPND 11 FRAGMENT: CR56; COMPND 12 SYNONYM: LRP, ALPHA-2-MACROGLOBULIN RECEPTOR; COMPND 13 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: LRPAP1, A2MRAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: LRP1; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, SHIFT-MAPPING, HADDOCK, INTERFACE, SURFACE ACTIVE PROTEIN EXPDTA SOLUTION NMR AUTHOR G.A.JENSEN,O.M.ANDERSEN,A.M.BONVIN,I.BJERRUM-BOHR,M.ETZERODT, AUTHOR 2 C.O'SHEA,F.M.POULSEN,B.B.KRAGELUND REVDAT 3 09-MAR-22 2FYL 1 REMARK LINK REVDAT 2 24-FEB-09 2FYL 1 VERSN REVDAT 1 10-OCT-06 2FYL 0 JRNL AUTH G.A.JENSEN,O.M.ANDERSEN,A.M.BONVIN,I.BJERRUM-BOHR, JRNL AUTH 2 M.ETZERODT,C.O'SHEA,F.M.POULSEN,B.B.KRAGELUND JRNL TITL BINDING SITE STRUCTURE OF ONE LRP-RAP COMPLEX:IMPLICATIONS JRNL TITL 2 FOR A COMMON LIGAND-RECEPTOR BINDING MOTIF. JRNL REF J.MOL.BIOL. V. 362 700 2006 JRNL REFN ISSN 0022-2836 JRNL PMID 16938309 JRNL DOI 10.1016/J.JMB.2006.07.013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PRONTO3D 20020517, HADDOCK REMARK 3 AUTHORS : KJAER ET AL (PRONTO3D), BONVIN ET AL (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2FYL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-FEB-06. REMARK 100 THE DEPOSITION ID IS D_1000036465. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.1MM [U-99% 15N]-CR56; 0.1MM REMARK 210 RAPD1; H2O/D2O (90:10); 0.5MM [U- REMARK 210 99% 15N]-RAPD1; 0.5MM CR56; H2O/ REMARK 210 D2O (90:10); 0.08 MM [U-99% 15N, REMARK 210 U-99% 13C]-CR56; 0.08 MM [U-99% REMARK 210 15N, U-99% 13C]-RAPD1; H2O/D2O REMARK 210 (90:10) REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : EXCHANGE 15N,1H-HSQC; EXCHANGE REMARK 210 15N,1H,-HSQC; HNCA; HNCACB, REMARK 210 HN(CO)CACB REMARK 210 SPECTROMETER FIELD STRENGTH : 750 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : HADDOCK REMARK 210 METHOD USED : HADDOCK MODELLING FROM CHEMICAL REMARK 210 SHIFT PERTURBATION DATA ON BOTH REMARK 210 COMPLEX PARTNERS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : BEST AVERAGED HADDOCK SCORE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 5 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 HZ3 LYS A 93 OD2 ASP B 66 1.57 REMARK 500 OE2 GLU A 30 HH12 ARG B 57 1.58 REMARK 500 OD2 ASP A 91 HZ3 LYS A 94 1.59 REMARK 500 HZ3 LYS A 60 OD1 ASP B 27 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS B 65 CB CYS B 65 SG -0.656 REMARK 500 ASN B 69 CG ASN B 69 OD1 1.283 REMARK 500 ASN B 69 CG ASN B 69 ND2 1.009 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 ASP A 65 CB - CG - OD1 ANGL. DEV. = -22.9 DEGREES REMARK 500 GLU A 69 CG - CD - OE2 ANGL. DEV. = -95.2 DEGREES REMARK 500 ASP B 32 CB - CG - OD1 ANGL. DEV. = -14.9 DEGREES REMARK 500 ASP B 32 CB - CG - OD2 ANGL. DEV. = 12.2 DEGREES REMARK 500 CYS B 65 CA - CB - SG ANGL. DEV. = -79.2 DEGREES REMARK 500 ASN B 69 OD1 - CG - ND2 ANGL. DEV. = -67.1 DEGREES REMARK 500 ASN B 69 CB - CG - ND2 ANGL. DEV. = 40.7 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 HIS A 36 106.68 70.88 REMARK 500 ASP A 95 -58.18 -161.21 REMARK 500 CYS B 5 148.94 70.40 REMARK 500 ALA B 13 -71.94 -24.77 REMARK 500 SER B 14 34.40 -80.76 REMARK 500 ARG B 16 -156.31 -84.89 REMARK 500 THR B 23 -99.51 -58.39 REMARK 500 ASP B 25 -52.12 -140.71 REMARK 500 LEU B 26 -20.58 161.62 REMARK 500 ASP B 29 -108.72 -96.32 REMARK 500 CYS B 30 30.65 -169.62 REMARK 500 ARG B 33 -42.13 -158.65 REMARK 500 SER B 37 -55.04 81.80 REMARK 500 ALA B 38 41.89 -79.87 REMARK 500 SER B 39 -64.18 -144.80 REMARK 500 ALA B 41 -2.11 72.07 REMARK 500 TYR B 42 73.29 55.20 REMARK 500 CYS B 45 -71.28 68.55 REMARK 500 PHE B 46 107.84 -169.22 REMARK 500 PRO B 47 45.21 -85.02 REMARK 500 CYS B 53 -164.16 -72.14 REMARK 500 ASN B 54 98.86 -29.72 REMARK 500 ASN B 62 48.53 -100.97 REMARK 500 ARG B 64 -73.76 -54.14 REMARK 500 CYS B 65 -68.15 66.67 REMARK 500 ASP B 68 -163.94 -114.55 REMARK 500 ASP B 70 -140.18 -80.89 REMARK 500 CYS B 71 150.14 -40.43 REMARK 500 GLU B 77 -59.41 -166.60 REMARK 500 SER B 81 -71.25 -62.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 65 0.17 SIDE CHAIN REMARK 500 GLU A 69 0.19 SIDE CHAIN REMARK 500 ASN B 69 0.15 SIDE CHAIN 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 B 83 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 22 O REMARK 620 2 THR B 23 O 80.7 REMARK 620 3 ASP B 25 OD1 81.3 90.2 REMARK 620 4 ASP B 27 O 136.2 141.8 87.4 REMARK 620 5 ASP B 29 OD1 70.9 138.2 114.1 75.8 REMARK 620 6 ASP B 35 OD1 84.6 78.9 163.4 108.9 68.7 REMARK 620 7 GLU B 36 OE2 133.3 70.9 63.0 74.1 149.9 123.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 84 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TRP B 63 O REMARK 620 2 ARG B 64 O 69.1 REMARK 620 3 ASP B 66 OD1 145.9 76.8 REMARK 620 4 ASP B 70 OD1 85.2 113.5 107.7 REMARK 620 5 ASP B 76 OD1 60.9 130.0 153.1 63.0 REMARK 620 6 GLU B 77 OE2 120.6 90.2 59.5 150.8 115.2 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 B 83 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 84 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FYJ RELATED DB: PDB REMARK 900 CR56 REMARK 900 RELATED ID: 1LRE RELATED DB: PDB REMARK 900 RAP-D1 DBREF 2FYL A 17 97 UNP P30533 AMRP_HUMAN 51 131 DBREF 2FYL B 1 82 UNP Q07954 LRP1_HUMAN 932 1013 SEQRES 1 A 81 GLY GLU GLU PHE ARG MET GLU LYS LEU ASN GLN LEU TRP SEQRES 2 A 81 GLU LYS ALA GLN ARG LEU HIS LEU PRO PRO VAL ARG LEU SEQRES 3 A 81 ALA GLU LEU HIS ALA ASP LEU LYS ILE GLN GLU ARG ASP SEQRES 4 A 81 GLU LEU ALA TRP LYS LYS LEU LYS LEU ASP GLY LEU ASP SEQRES 5 A 81 GLU ASP GLY GLU LYS GLU ALA ARG LEU ILE ARG ASN LEU SEQRES 6 A 81 ASN VAL ILE LEU ALA LYS TYR GLY LEU ASP GLY LYS LYS SEQRES 7 A 81 ASP ALA ARG SEQRES 1 B 82 SER ALA ARG THR CYS PRO PRO ASN GLN PHE SER CYS ALA SEQRES 2 B 82 SER GLY ARG CYS ILE PRO ILE SER TRP THR CYS ASP LEU SEQRES 3 B 82 ASP ASP ASP CYS GLY ASP ARG SER ASP GLU SER ALA SER SEQRES 4 B 82 CYS ALA TYR PRO THR CYS PHE PRO LEU THR GLN PHE THR SEQRES 5 B 82 CYS ASN ASN GLY ARG CYS ILE ASN ILE ASN TRP ARG CYS SEQRES 6 B 82 ASP ASN ASP ASN ASP CYS GLY ASP ASN SER ASP GLU ALA SEQRES 7 B 82 GLY CYS SER HIS HET CA B 83 1 HET CA B 84 1 HETNAM CA CALCIUM ION FORMUL 3 CA 2(CA 2+) HELIX 1 1 MET A 22 LEU A 35 1 14 HELIX 2 2 PRO A 38 GLY A 66 1 29 HELIX 3 3 GLY A 71 GLY A 89 1 19 HELIX 4 4 SER B 21 THR B 23 5 3 SHEET 1 A 2 GLN B 9 PHE B 10 0 SHEET 2 A 2 ILE B 18 PRO B 19 -1 O ILE B 18 N PHE B 10 SHEET 1 B 2 GLN B 50 CYS B 53 0 SHEET 2 B 2 ARG B 57 ASN B 60 -1 O ILE B 59 N PHE B 51 SSBOND 1 CYS B 5 CYS B 17 1555 1555 2.03 SSBOND 2 CYS B 12 CYS B 30 1555 1555 2.04 SSBOND 3 CYS B 24 CYS B 40 1555 1555 2.02 SSBOND 4 CYS B 45 CYS B 58 1555 1555 2.03 SSBOND 5 CYS B 53 CYS B 71 1555 1555 2.03 LINK O TRP B 22 CA CA B 83 1555 1555 1.91 LINK O THR B 23 CA CA B 83 1555 1555 1.97 LINK OD1 ASP B 25 CA CA B 83 1555 1555 2.52 LINK O ASP B 27 CA CA B 83 1555 1555 2.10 LINK OD1 ASP B 29 CA CA B 83 1555 1555 2.52 LINK OD1 ASP B 35 CA CA B 83 1555 1555 2.51 LINK OE2 GLU B 36 CA CA B 83 1555 1555 2.52 LINK O TRP B 63 CA CA B 84 1555 1555 2.86 LINK O ARG B 64 CA CA B 84 1555 1555 1.82 LINK OD1 ASP B 66 CA CA B 84 1555 1555 2.51 LINK OD1 ASP B 70 CA CA B 84 1555 1555 2.51 LINK OD1 ASP B 76 CA CA B 84 1555 1555 2.49 LINK OE2 GLU B 77 CA CA B 84 1555 1555 2.50 SITE 1 AC1 7 TRP B 22 THR B 23 ASP B 25 ASP B 27 SITE 2 AC1 7 ASP B 29 ASP B 35 GLU B 36 SITE 1 AC2 6 TRP B 63 ARG B 64 ASP B 66 ASP B 70 SITE 2 AC2 6 ASP B 76 GLU B 77 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