PDB Short entry for 2M1K HEADER PROTEIN BINDING 29-NOV-12 2M1K TITLE INTERACTION OF HUMAN S100A6 (C3S) WITH V DOMAIN OF RECEPTOR FOR TITLE 2 ADVANCED GLYCATION END PRODUCTS (RAGE) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN S100-A6; COMPND 3 CHAIN: B, D; COMPND 4 SYNONYM: CALCYCLIN, GROWTH FACTOR-INDUCIBLE PROTEIN 2A9, MLN 4, COMPND 5 PROLACTIN RECEPTOR-ASSOCIATED PROTEIN, PRA, S100 CALCIUM-BINDING COMPND 6 PROTEIN A6; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: ADVANCED GLYCOSYLATION END PRODUCT-SPECIFIC RECEPTOR; COMPND 11 CHAIN: A, C; COMPND 12 FRAGMENT: UNP RESIDUES 23-121; COMPND 13 SYNONYM: RECEPTOR FOR ADVANCED GLYCOSYLATION END PRODUCTS; COMPND 14 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: CACY, S100A6; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET(20B)+; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 13 ORGANISM_COMMON: HUMAN; SOURCE 14 ORGANISM_TAXID: 9606; SOURCE 15 GENE: AGER, RAGE; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PET(15B)+ KEYWDS S100A6 C3S, RAGE V, HETEROTETRAMERIC, HADDOCK MODEL, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.A.GUPTA,C.YU REVDAT 2 14-JUN-23 2M1K 1 REMARK SEQADV REVDAT 1 25-MAR-15 2M1K 0 JRNL AUTH S.K.MOHAN,A.A.GUPTA,C.YU JRNL TITL INTERACTION OF THE S100A6 MUTANT (C3S) WITH THE V DOMAIN OF JRNL TITL 2 THE RECEPTOR FOR ADVANCED GLYCATION END PRODUCTS (RAGE). JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 434 328 2013 JRNL REFN ISSN 0006-291X JRNL PMID 23537648 JRNL DOI 10.1016/J.BBRC.2013.03.049 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMRJ 2.3, HADDOCK REMARK 3 AUTHORS : VARIAN (VNMRJ), ALEXANDRE BONVIN (HADDOCK) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HADDOCK STARTING STRUCTURES ARE PDB REMARK 3 ENTRIES 1K9K AND 2E5E. MODELS 1-10 ARE SUPERIMPOSED, WHILE REMARK 3 MODELS 11-20 ARE SUPERIMPOSED IN A DIFFERENT ORIENTATION. REMARK 4 REMARK 4 2M1K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000103092. 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 : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 S100A6 C3S, 20 MM TRIS, 10 MM REMARK 210 CALCIUM CHLORIDE, 0.01 % SODIUM REMARK 210 AZIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HN(CO)CA; 3D HNCACB; 3D CBCA(CO) REMARK 210 NH; 3D HNCO; 3D HCACO REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMRJ 2.3, SPARKY, HADDOCK REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 23380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, A, C 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET B 1 REMARK 465 MET D 1 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 LYS D 64 70.92 59.62 REMARK 500 1 LYS A 39 -176.16 -65.39 REMARK 500 1 PRO A 42 -173.56 -61.38 REMARK 500 1 PRO A 46 105.67 -55.35 REMARK 500 1 THR A 58 104.85 62.10 REMARK 500 1 GLU A 59 16.70 -140.91 REMARK 500 1 ALA A 88 105.45 -167.55 REMARK 500 1 GLU A 94 178.17 -50.86 REMARK 500 1 ASN A 103 -161.19 -100.81 REMARK 500 1 ASN A 105 -76.38 -107.44 REMARK 500 1 TYR A 118 -78.05 -52.94 REMARK 500 1 LYS C 39 -176.19 -65.20 REMARK 500 1 PRO C 42 -174.84 -61.62 REMARK 500 1 PRO C 46 105.51 -55.33 REMARK 500 1 THR C 58 104.87 62.07 REMARK 500 1 GLU C 59 16.61 -140.97 REMARK 500 1 ALA C 88 105.58 -167.48 REMARK 500 1 GLU C 94 178.06 -50.83 REMARK 500 1 ASN C 103 -161.90 -101.51 REMARK 500 1 ASN C 105 -73.22 -102.09 REMARK 500 1 TYR C 118 -77.95 -52.96 REMARK 500 2 LYS B 64 73.91 61.52 REMARK 500 2 LYS D 64 80.41 60.15 REMARK 500 2 LYS A 39 -176.18 -65.28 REMARK 500 2 PRO A 42 -172.20 -62.94 REMARK 500 2 PRO A 46 105.71 -55.34 REMARK 500 2 THR A 58 104.91 62.13 REMARK 500 2 GLU A 59 16.65 -141.00 REMARK 500 2 ALA A 88 105.51 -167.49 REMARK 500 2 GLU A 94 178.13 -50.90 REMARK 500 2 TYR A 118 -77.97 -53.03 REMARK 500 2 LYS C 39 -176.09 -65.39 REMARK 500 2 PRO C 42 -172.04 -62.85 REMARK 500 2 PRO C 46 105.51 -55.16 REMARK 500 2 THR C 58 104.84 62.05 REMARK 500 2 GLU C 59 16.74 -140.96 REMARK 500 2 ALA C 88 105.54 -167.53 REMARK 500 2 GLU C 94 178.18 -51.04 REMARK 500 2 TYR C 118 -78.00 -53.00 REMARK 500 3 LYS B 64 73.85 65.50 REMARK 500 3 LYS D 64 77.91 60.80 REMARK 500 3 PRO A 42 -173.81 -61.61 REMARK 500 3 PRO A 46 105.65 -55.39 REMARK 500 3 THR A 58 104.84 62.21 REMARK 500 3 GLU A 59 16.61 -140.94 REMARK 500 3 ALA A 88 105.49 -167.49 REMARK 500 3 GLU A 94 178.13 -50.80 REMARK 500 3 TYR A 118 -78.07 -52.96 REMARK 500 3 LYS C 39 -176.10 -65.29 REMARK 500 3 PRO C 42 -173.02 -60.99 REMARK 500 REMARK 500 THIS ENTRY HAS 311 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18868 RELATED DB: BMRB REMARK 900 RELATED ID: 1K9K RELATED DB: PDB REMARK 900 HADDOCK STARTING STRUCTURE REMARK 900 RELATED ID: 2E5E RELATED DB: PDB REMARK 900 HADDOCK STARTING STRUCTURE DBREF 2M1K B 1 90 UNP P06703 S10A6_HUMAN 1 90 DBREF 2M1K D 1 90 UNP P06703 S10A6_HUMAN 1 90 DBREF 2M1K A 23 121 UNP Q15109 RAGE_HUMAN 23 121 DBREF 2M1K C 23 121 UNP Q15109 RAGE_HUMAN 23 121 SEQADV 2M1K SER B 3 UNP P06703 CYS 3 ENGINEERED MUTATION SEQADV 2M1K SER D 3 UNP P06703 CYS 3 ENGINEERED MUTATION SEQADV 2M1K ALA A 21 UNP Q15109 EXPRESSION TAG SEQADV 2M1K MET A 22 UNP Q15109 EXPRESSION TAG SEQADV 2M1K ALA C 21 UNP Q15109 EXPRESSION TAG SEQADV 2M1K MET C 22 UNP Q15109 EXPRESSION TAG SEQRES 1 B 90 MET ALA SER PRO LEU ASP GLN ALA ILE GLY LEU LEU VAL SEQRES 2 B 90 ALA ILE PHE HIS LYS TYR SER GLY ARG GLU GLY ASP LYS SEQRES 3 B 90 HIS THR LEU SER LYS LYS GLU LEU LYS GLU LEU ILE GLN SEQRES 4 B 90 LYS GLU LEU THR ILE GLY SER LYS LEU GLN ASP ALA GLU SEQRES 5 B 90 ILE ALA ARG LEU MET GLU ASP LEU ASP ARG ASN LYS ASP SEQRES 6 B 90 GLN GLU VAL ASN PHE GLN GLU TYR VAL THR PHE LEU GLY SEQRES 7 B 90 ALA LEU ALA LEU ILE TYR ASN GLU ALA LEU LYS GLY SEQRES 1 D 90 MET ALA SER PRO LEU ASP GLN ALA ILE GLY LEU LEU VAL SEQRES 2 D 90 ALA ILE PHE HIS LYS TYR SER GLY ARG GLU GLY ASP LYS SEQRES 3 D 90 HIS THR LEU SER LYS LYS GLU LEU LYS GLU LEU ILE GLN SEQRES 4 D 90 LYS GLU LEU THR ILE GLY SER LYS LEU GLN ASP ALA GLU SEQRES 5 D 90 ILE ALA ARG LEU MET GLU ASP LEU ASP ARG ASN LYS ASP SEQRES 6 D 90 GLN GLU VAL ASN PHE GLN GLU TYR VAL THR PHE LEU GLY SEQRES 7 D 90 ALA LEU ALA LEU ILE TYR ASN GLU ALA LEU LYS GLY SEQRES 1 A 101 ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU PRO SEQRES 2 A 101 LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO PRO SEQRES 3 A 101 GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR GLU SEQRES 4 A 101 ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO TRP SEQRES 5 A 101 ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU PHE SEQRES 6 A 101 LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE ARG SEQRES 7 A 101 CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SER SEQRES 8 A 101 ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO SEQRES 1 C 101 ALA MET ALA GLN ASN ILE THR ALA ARG ILE GLY GLU PRO SEQRES 2 C 101 LEU VAL LEU LYS CYS LYS GLY ALA PRO LYS LYS PRO PRO SEQRES 3 C 101 GLN ARG LEU GLU TRP LYS LEU ASN THR GLY ARG THR GLU SEQRES 4 C 101 ALA TRP LYS VAL LEU SER PRO GLN GLY GLY GLY PRO TRP SEQRES 5 C 101 ASP SER VAL ALA ARG VAL LEU PRO ASN GLY SER LEU PHE SEQRES 6 C 101 LEU PRO ALA VAL GLY ILE GLN ASP GLU GLY ILE PHE ARG SEQRES 7 C 101 CYS GLN ALA MET ASN ARG ASN GLY LYS GLU THR LYS SER SEQRES 8 C 101 ASN TYR ARG VAL ARG VAL TYR GLN ILE PRO HELIX 1 1 SER B 3 GLY B 21 1 19 HELIX 2 2 SER B 30 LEU B 42 1 13 HELIX 3 3 ILE B 44 LEU B 48 5 5 HELIX 4 4 GLN B 49 ASP B 61 1 13 HELIX 5 5 ASN B 69 GLY B 90 1 22 HELIX 6 6 SER D 3 GLY D 21 1 19 HELIX 7 7 SER D 30 LEU D 42 1 13 HELIX 8 8 ILE D 44 LEU D 48 5 5 HELIX 9 9 GLN D 49 ASP D 61 1 13 HELIX 10 10 ASN D 69 GLY D 90 1 22 HELIX 11 11 PRO A 71 ALA A 76 1 6 HELIX 12 12 PRO C 71 ALA C 76 1 6 SHEET 1 A 4 GLN A 24 ALA A 28 0 SHEET 2 A 4 ASN A 112 VAL A 117 1 O ARG A 114 N ILE A 26 SHEET 3 A 4 GLY A 95 MET A 102 -1 N GLY A 95 O VAL A 115 SHEET 4 A 4 ARG A 48 ASN A 54 -1 N GLU A 50 O GLN A 100 SHEET 1 B 2 GLU A 32 LYS A 37 0 SHEET 2 B 2 SER A 83 VAL A 89 -1 O LEU A 84 N LEU A 36 SHEET 1 C 4 GLN C 24 ALA C 28 0 SHEET 2 C 4 ASN C 112 VAL C 117 1 O ARG C 114 N ILE C 26 SHEET 3 C 4 GLY C 95 MET C 102 -1 N GLY C 95 O VAL C 115 SHEET 4 C 4 ARG C 48 ASN C 54 -1 N GLU C 50 O GLN C 100 SHEET 1 D 2 GLU C 32 LYS C 37 0 SHEET 2 D 2 SER C 83 VAL C 89 -1 O LEU C 84 N LEU C 36 SSBOND 1 CYS A 38 CYS A 99 1555 1555 2.03 SSBOND 2 CYS C 38 CYS C 99 1555 1555 2.03 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