10 20 30 40 50 60 70 80 2KMX - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 05-AUG-09 2KMX
TITLE SOLUTION STRUCTURE OF THE NUCLEOTIDE BINDING DOMAIN OF THE TITLE 2 HUMAN MENKES PROTEIN IN THE ATP-BOUND FORM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-TRANSPORTING ATPASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOTIDE BINDING DOMAIN; COMPND 5 SYNONYM: COPPER PUMP 1, MENKES DISEASE-ASSOCIATED PROTEIN; COMPND 6 EC: 3.6.3.4; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_TAXID: 9606; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA2; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETG-30A
KEYWDS ATP7A, MENKES, NMR, ATPASE, NUCLEOTIDE BINDING PROTEIN, KEYWDS 2 ALTERNATIVE SPLICING, ATP-BINDING, CELL MEMBRANE, COPPER, KEYWDS 3 COPPER TRANSPORT, CYTOPLASM, DISEASE MUTATION, ENDOPLASMIC KEYWDS 4 RETICULUM, GLYCOPROTEIN, GOLGI APPARATUS, HYDROLASE, ION KEYWDS 5 TRANSPORT, MAGNESIUM, MEMBRANE, METAL-BINDING, NUCLEOTIDE- KEYWDS 6 BINDING, PHOSPHOPROTEIN, POLYMORPHISM, TRANSMEMBRANE, KEYWDS 7 TRANSPORT
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR L.BANCI,I.BERTINI,F.CANTINI,S.INAGAKI,M.MIGLIARDI,A.ROSATO
REVDAT 1 01-DEC-09 2KMX 0
JRNL AUTH L.BANCI,I.BERTINI,F.CANTINI,S.INAGAKI,M.MIGLIARDI, JRNL AUTH 2 A.ROSATO JRNL TITL THE BINDING MODE OF ATP REVEALED BY THE SOLUTION JRNL TITL 2 STRUCTURE OF THE N-DOMAIN OF HUMAN ATP7A. JRNL REF J.BIOL.CHEM. 2009 JRNL REFN ESSN 1083-351X JRNL PMID 19917612 JRNL DOI 10.1074/JBC.M109.054262
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KMX COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-SEP-09. REMARK 100 THE RCSB ID CODE IS RCSB101319.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : PHOSPATE 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-99% 15N] ATPFREE N- REMARK 210 MNK-1, 90% H2O/10% D2O; 0.8 MM REMARK 210 [U-95% 13C; U-95% 15N] ATPFREE REMARK 210 N-MNK-2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 2D 1H-1H TOCSY; 2D 1H-1H REMARK 210 NOESY; 3D HNCO; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA, XEASY, CYANA, REMARK 210 PSVS, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 1 ARG A1190 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 1 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 2 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 2 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 3 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 4 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 4 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A1190 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 5 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 5 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 6 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 7 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 7 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 7 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 8 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 10 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 11 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 11 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 13 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 14 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 14 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 15 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 15 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 15 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 16 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 16 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 16 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 63 ANGLE DEVIATIONS. 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 MET A1050 32.02 -160.60 REMARK 500 1 SER A1065 -8.62 61.65 REMARK 500 1 ARG A1067 -66.28 -150.04 REMARK 500 1 THR A1102 -30.80 -138.88 REMARK 500 1 GLU A1103 -26.41 64.47 REMARK 500 1 THR A1104 45.20 -84.57 REMARK 500 1 ASN A1125 -42.44 -168.53 REMARK 500 1 GLU A1127 45.10 -150.24 REMARK 500 1 HIS A1131 115.02 64.58 REMARK 500 1 ASN A1140 98.88 -35.50 REMARK 500 1 LYS A1143 116.73 -169.78 REMARK 500 1 ASN A1144 36.57 -81.98 REMARK 500 1 LEU A1147 -12.47 -156.29 REMARK 500 1 ASN A1154 81.00 51.65 REMARK 500 1 THR A1159 148.98 61.61 REMARK 500 1 ILE A1164 -37.03 67.45 REMARK 500 1 ASP A1166 -20.39 60.78 REMARK 500 1 ASN A1184 -141.36 48.11 REMARK 500 1 ARG A1185 -32.58 -143.43 REMARK 500 1 ASN A1191 20.23 -72.76 REMARK 500 2 PHE A1048 16.00 54.71 REMARK 500 2 ASN A1066 -14.70 -145.55 REMARK 500 2 ARG A1067 -97.53 -149.65 REMARK 500 2 THR A1107 -37.43 -152.51 REMARK 500 2 PHE A1111 96.99 45.26 REMARK 500 2 CYS A1117 -87.77 -137.48 REMARK 500 2 ASN A1125 -42.55 -175.56 REMARK 500 2 HIS A1131 73.24 40.71 REMARK 500 2 TRP A1135 -22.64 -155.85 REMARK 500 2 ALA A1145 -87.09 -137.18 REMARK 500 2 SER A1146 -45.43 68.16 REMARK 500 2 LEU A1147 -116.34 45.80 REMARK 500 2 GLN A1149 32.80 -71.27 REMARK 500 2 ILE A1150 -29.92 -143.45 REMARK 500 2 SER A1153 136.16 57.93 REMARK 500 2 GLN A1176 129.28 46.20 REMARK 500 2 ASN A1184 -159.46 51.64 REMARK 500 2 ARG A1190 -13.15 -47.70 REMARK 500 3 HIS A1051 -31.83 -141.37 REMARK 500 3 SER A1065 -50.91 61.32 REMARK 500 3 ARG A1067 -53.85 64.34 REMARK 500 3 GLU A1085 46.87 -141.20 REMARK 500 3 CYS A1117 -47.90 -146.52 REMARK 500 3 ASN A1125 59.37 148.09 REMARK 500 3 ILE A1126 -67.73 -148.35 REMARK 500 3 LEU A1129 -7.83 -57.39 REMARK 500 3 HIS A1131 64.75 31.24 REMARK 500 3 ASN A1134 119.52 60.70 REMARK 500 3 TRP A1135 -19.10 -141.62 REMARK 500 3 ASN A1141 -34.38 -159.84 REMARK 500 REMARK 500 THIS ENTRY HAS 368 RAMACHANDRAN OUTLIERS. 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 3 PHE A1111 0.09 SIDE CHAIN REMARK 500 5 ARG A1185 0.10 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 12 SER A1158 24.9 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 1232
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KMV RELATED DB: PDB REMARK 900 ATP-FREE N- DOMAIN REMARK 900 RELATED ID: 16441 RELATED DB: BMRB REMARK 900 ATP-FREE N- DOMAIN
DBREF 2KMX A 1051 1231 UNP Q04656 ATP7A_HUMAN 1051 1231
SEQADV 2KMX SER A 1047 UNP Q04656 EXPRESSION TAG SEQADV 2KMX PHE A 1048 UNP Q04656 EXPRESSION TAG SEQADV 2KMX THR A 1049 UNP Q04656 EXPRESSION TAG SEQADV 2KMX MET A 1050 UNP Q04656 EXPRESSION TAG
SEQRES 1 A 185 SER PHE THR MET HIS GLY THR PRO VAL VAL ASN GLN VAL SEQRES 2 A 185 LYS VAL LEU THR GLU SER ASN ARG ILE SER HIS HIS LYS SEQRES 3 A 185 ILE LEU ALA ILE VAL GLY THR ALA GLU SER ASN SER GLU SEQRES 4 A 185 HIS PRO LEU GLY THR ALA ILE THR LYS TYR CYS LYS GLN SEQRES 5 A 185 GLU LEU ASP THR GLU THR LEU GLY THR CYS ILE ASP PHE SEQRES 6 A 185 GLN VAL VAL PRO GLY CYS GLY ILE SER CYS LYS VAL THR SEQRES 7 A 185 ASN ILE GLU GLY LEU LEU HIS LYS ASN ASN TRP ASN ILE SEQRES 8 A 185 GLU ASP ASN ASN ILE LYS ASN ALA SER LEU VAL GLN ILE SEQRES 9 A 185 ASP ALA SER ASN GLU GLN SER SER THR SER SER SER MET SEQRES 10 A 185 ILE ILE ASP ALA GLN ILE SER ASN ALA LEU ASN ALA GLN SEQRES 11 A 185 GLN TYR LYS VAL LEU ILE GLY ASN ARG GLU TRP MET ILE SEQRES 12 A 185 ARG ASN GLY LEU VAL ILE ASN ASN ASP VAL ASN ASP PHE SEQRES 13 A 185 MET THR GLU HIS GLU ARG LYS GLY ARG THR ALA VAL LEU SEQRES 14 A 185 VAL ALA VAL ASP ASP GLU LEU CYS GLY LEU ILE ALA ILE SEQRES 15 A 185 ALA ASP THR
HET ATP A1232 43
HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE
FORMUL 2 ATP C10 H16 N5 O13 P3
HELIX 1 1 SER A 1069 SER A 1082 1 14 HELIX 2 2 GLY A 1089 ASP A 1101 1 13 HELIX 3 3 GLU A 1127 HIS A 1131 5 5 HELIX 4 4 GLN A 1149 SER A 1153 5 5 HELIX 5 5 GLN A 1168 ALA A 1175 1 8 HELIX 6 6 ARG A 1185 ASN A 1191 1 7 HELIX 7 7 ASN A 1196 LYS A 1209 1 14
SHEET 1 A 6 PRO A1054 VAL A1061 0 SHEET 2 A 6 GLU A1221 ASP A1230 -1 O ALA A1227 N GLN A1058 SHEET 3 A 6 THR A1212 VAL A1218 -1 N VAL A1218 O GLU A1221 SHEET 4 A 6 GLN A1177 ILE A1182 -1 N LEU A1181 O ALA A1217 SHEET 5 A 6 GLY A1118 THR A1124 -1 N CYS A1121 O VAL A1180 SHEET 6 A 6 ILE A1109 VAL A1114 -1 N GLN A1112 O SER A1120
SITE 1 AC1 11 GLU A1081 HIS A1086 PRO A1087 LEU A1088 SITE 2 AC1 11 GLY A1089 GLY A1116 GLY A1118 ILE A1182 SITE 3 AC1 11 GLY A1183 ASN A1184 VAL A1214
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