10 20 30 40 50 60 70 80 1WGO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 28-MAY-04 1WGO
TITLE SOLUTION STRUCTURE OF THE PKD DOMAIN FROM HUMAN VPS10 TITLE 2 DOMAIN-CONTAINING RECEPTOR SORCS2
COMPND MOL_ID: 1; COMPND 2 MOLECULE: VPS10 DOMAIN-CONTAINING RECEPTOR SORCS2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PKD DOMAIN; COMPND 5 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: KAZUSA CDNA FH14788; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P040119-67; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS
KEYWDS POLYCYSTIC KIDNEY DISEASE, PKD, STRUCTURAL GENOMICS, KEYWDS 2 KIAA1329 PROTEIN, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 3 INITIATIVE, RSGI, MEMBRANE PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR E.CHIKAYAMA,T.KIGAWA,N.TOCHIO,S.KOSHIBA,M.INOUE,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI)
REVDAT 2 24-FEB-09 1WGO 1 VERSN REVDAT 1 28-NOV-04 1WGO 0
JRNL AUTH E.CHIKAYAMA,T.KIGAWA,N.TOCHIO,S.KOSHIBA,M.INOUE, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE PKD DOMAIN FROM HUMAN JRNL TITL 2 VPS10 DOMAIN-CONTAINING RECEPTOR SORCS2 JRNL REF TO BE PUBLISHED JRNL REFN
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA 2.0.17 REMARK 3 AUTHORS : GUENTERT, P. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1WGO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-JUN-04. REMARK 100 THE RCSB ID CODE IS RCSB023559.
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 : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.12MM PKD DOMAIN U-15N, 13C; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, NMRPIPE REMARK 210 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.901, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 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, TARGET FUNCTION 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: 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 CYS A 8 136.81 -171.28 REMARK 500 1 ASP A 13 158.15 -45.76 REMARK 500 1 MET A 14 85.67 -65.81 REMARK 500 1 GLN A 18 60.46 -100.96 REMARK 500 1 LEU A 21 127.68 -174.16 REMARK 500 1 VAL A 40 -66.82 -95.00 REMARK 500 1 VAL A 59 156.77 -47.24 REMARK 500 1 THR A 61 105.83 -39.53 REMARK 500 1 ASP A 70 40.01 -91.25 REMARK 500 1 GLU A 91 -60.58 -102.35 REMARK 500 1 ALA A 106 -74.86 -94.04 REMARK 500 1 PRO A 120 2.73 -69.71 REMARK 500 1 SER A 122 159.30 -42.82 REMARK 500 2 GLN A 15 93.86 -69.33 REMARK 500 2 LEU A 21 137.07 -36.87 REMARK 500 2 PRO A 24 87.94 -69.76 REMARK 500 2 GLN A 36 103.62 -38.81 REMARK 500 2 GLU A 38 107.82 -59.41 REMARK 500 2 LEU A 60 -179.62 -52.03 REMARK 500 2 HIS A 88 118.02 -165.04 REMARK 500 2 ALA A 106 -72.26 -62.76 REMARK 500 2 PRO A 120 81.74 -69.81 REMARK 500 3 GLN A 36 93.24 -39.10 REMARK 500 3 GLU A 38 109.11 -59.93 REMARK 500 3 VAL A 59 35.50 32.55 REMARK 500 3 THR A 61 102.47 -55.83 REMARK 500 3 ALA A 106 -71.95 -63.76 REMARK 500 4 GLN A 15 42.15 35.73 REMARK 500 4 PRO A 24 92.22 -69.77 REMARK 500 4 PRO A 28 95.07 -69.73 REMARK 500 4 GLN A 36 96.86 -35.03 REMARK 500 4 ASP A 47 87.45 -57.87 REMARK 500 4 LEU A 60 144.59 -36.94 REMARK 500 4 ASN A 78 37.79 34.60 REMARK 500 4 ALA A 106 -73.98 -61.33 REMARK 500 5 MET A 14 141.68 -174.54 REMARK 500 5 GLN A 20 152.56 -47.76 REMARK 500 5 PRO A 24 -173.48 -69.79 REMARK 500 5 GLN A 36 100.17 -34.22 REMARK 500 5 GLU A 38 107.92 -56.50 REMARK 500 5 PRO A 44 86.00 -69.81 REMARK 500 5 VAL A 59 25.02 39.97 REMARK 500 5 ASP A 70 -74.77 -45.90 REMARK 500 5 PRO A 120 93.71 -69.76 REMARK 500 5 SER A 122 -53.99 -127.52 REMARK 500 6 SER A 6 166.90 -45.10 REMARK 500 6 GLN A 15 -46.46 -132.47 REMARK 500 6 GLN A 16 43.43 34.81 REMARK 500 6 GLN A 18 42.18 -95.34 REMARK 500 6 PRO A 24 -172.45 -69.70 REMARK 500 6 GLN A 36 91.54 -45.54 REMARK 500 6 VAL A 40 -63.20 -94.71 REMARK 500 6 ASP A 47 95.44 -68.33 REMARK 500 6 PRO A 120 1.89 -69.71 REMARK 500 7 GLU A 9 130.70 -172.66 REMARK 500 7 ASP A 13 172.33 -49.54 REMARK 500 7 GLN A 36 105.37 -38.17 REMARK 500 7 GLU A 38 107.96 -57.41 REMARK 500 7 VAL A 59 -56.52 -132.98 REMARK 500 7 LEU A 60 142.66 -35.92 REMARK 500 7 GLU A 84 117.89 -34.94 REMARK 500 7 PRO A 85 -173.01 -69.74 REMARK 500 7 ALA A 106 -65.48 -93.33 REMARK 500 7 SER A 118 -176.17 -56.47 REMARK 500 7 SER A 121 -64.57 -90.54 REMARK 500 8 GLN A 20 128.90 -172.13 REMARK 500 8 PRO A 24 -171.63 -69.83 REMARK 500 8 GLN A 36 93.49 -34.66 REMARK 500 8 GLU A 38 107.68 -57.01 REMARK 500 8 SER A 118 -178.65 -65.78 REMARK 500 9 VAL A 12 112.98 -172.75 REMARK 500 9 GLN A 36 98.20 -44.40 REMARK 500 9 GLU A 38 109.28 -55.99 REMARK 500 9 VAL A 40 -61.76 -102.50 REMARK 500 9 PRO A 44 89.91 -69.81 REMARK 500 9 VAL A 59 148.39 -33.82 REMARK 500 9 THR A 61 123.33 -34.74 REMARK 500 9 ASP A 70 -70.81 -47.63 REMARK 500 10 SER A 3 112.33 -170.21 REMARK 500 10 SER A 5 117.04 -163.46 REMARK 500 10 CYS A 8 115.29 -162.18 REMARK 500 10 GLN A 36 100.83 -45.99 REMARK 500 10 GLU A 38 107.96 -58.72 REMARK 500 10 PRO A 44 93.17 -69.78 REMARK 500 10 ASN A 78 37.28 37.34 REMARK 500 10 ALA A 106 -70.33 -60.64 REMARK 500 10 SER A 122 103.13 -50.90 REMARK 500 11 SER A 5 128.41 -171.72 REMARK 500 11 CYS A 8 111.47 -166.76 REMARK 500 11 LEU A 25 -177.32 -56.03 REMARK 500 11 GLN A 36 94.16 -34.38 REMARK 500 11 GLU A 38 108.29 -56.27 REMARK 500 11 PRO A 44 86.38 -69.76 REMARK 500 11 ASP A 47 128.77 -37.91 REMARK 500 11 VAL A 59 -37.16 -38.59 REMARK 500 11 LEU A 60 122.93 -33.73 REMARK 500 11 THR A 61 109.56 -42.17 REMARK 500 11 ASN A 78 37.18 35.96 REMARK 500 11 ALA A 106 -73.48 -75.03 REMARK 500 11 PRO A 120 1.55 -69.82 REMARK 500 12 SER A 2 149.54 -174.54 REMARK 500 12 SER A 17 125.39 -172.79 REMARK 500 12 PRO A 24 -170.39 -69.81 REMARK 500 12 GLN A 36 94.75 -36.57 REMARK 500 12 VAL A 40 -62.85 -122.51 REMARK 500 12 ASP A 47 98.51 -59.07 REMARK 500 12 VAL A 59 139.08 -32.36 REMARK 500 12 ASP A 70 -70.05 -48.90 REMARK 500 12 ASN A 78 25.31 42.07 REMARK 500 12 ALA A 102 117.64 -161.08 REMARK 500 12 PRO A 120 85.60 -69.70 REMARK 500 13 VAL A 12 37.76 33.71 REMARK 500 13 GLN A 36 93.98 -35.54 REMARK 500 13 GLU A 38 107.84 -55.98 REMARK 500 13 PRO A 44 83.67 -69.75 REMARK 500 13 VAL A 59 151.14 -34.02 REMARK 500 13 LEU A 60 46.97 36.91 REMARK 500 13 THR A 61 143.02 -38.88 REMARK 500 13 ALA A 106 -70.99 -58.65 REMARK 500 13 PRO A 120 1.47 -69.74 REMARK 500 14 SER A 2 123.36 -171.54 REMARK 500 14 GLN A 36 99.34 -35.35 REMARK 500 14 GLU A 38 107.93 -59.38 REMARK 500 14 VAL A 40 -65.40 -106.04 REMARK 500 14 PRO A 44 99.14 -69.77 REMARK 500 14 GLU A 84 125.45 -39.50 REMARK 500 14 PRO A 85 -175.83 -69.82 REMARK 500 14 ALA A 106 -72.29 -62.34 REMARK 500 14 SER A 122 59.02 -116.36 REMARK 500 15 CYS A 8 -46.56 -131.10 REMARK 500 15 GLN A 18 45.51 -93.93 REMARK 500 15 PRO A 24 -171.24 -69.83 REMARK 500 15 GLN A 36 93.48 -34.86 REMARK 500 15 VAL A 40 -56.48 -124.82 REMARK 500 15 PRO A 44 85.59 -69.79 REMARK 500 15 VAL A 59 -51.18 -130.59 REMARK 500 15 LEU A 60 121.91 -34.99 REMARK 500 15 GLU A 84 122.11 -34.28 REMARK 500 15 PRO A 85 -171.73 -69.78 REMARK 500 15 SER A 118 167.85 -47.86 REMARK 500 15 PRO A 120 2.79 -69.76 REMARK 500 15 SER A 121 53.26 74.43 REMARK 500 16 LEU A 21 141.59 -172.09 REMARK 500 16 PRO A 24 -164.30 -69.73 REMARK 500 16 LEU A 25 149.87 -34.16 REMARK 500 16 GLN A 36 104.30 -36.44 REMARK 500 16 GLU A 38 107.88 -59.66 REMARK 500 16 ASP A 47 84.79 -53.92 REMARK 500 16 VAL A 59 124.08 -171.66 REMARK 500 16 ASP A 70 -71.62 -58.03 REMARK 500 16 ALA A 106 -71.12 -64.47 REMARK 500 16 PRO A 120 2.49 -69.75 REMARK 500 17 MET A 14 151.05 -42.75 REMARK 500 17 GLN A 15 -55.06 -121.55 REMARK 500 17 PRO A 24 -164.32 -69.77 REMARK 500 17 GLU A 38 107.85 -57.19 REMARK 500 17 VAL A 40 -57.65 -126.03 REMARK 500 17 PRO A 44 96.19 -69.74 REMARK 500 17 THR A 61 44.97 34.46 REMARK 500 17 ASN A 78 38.42 34.38 REMARK 500 17 SER A 118 174.11 -55.74 REMARK 500 18 GLN A 20 42.52 -102.37 REMARK 500 18 PRO A 24 2.60 -69.76 REMARK 500 18 GLN A 36 95.06 -42.02 REMARK 500 18 GLU A 38 107.81 -56.24 REMARK 500 18 VAL A 40 -63.73 -98.06 REMARK 500 18 VAL A 59 -52.35 -29.70 REMARK 500 18 THR A 61 101.11 -43.64 REMARK 500 18 GLU A 84 116.71 -35.52 REMARK 500 19 VAL A 19 36.46 35.32 REMARK 500 19 GLN A 36 97.91 -45.66 REMARK 500 19 GLU A 38 107.91 -56.02 REMARK 500 19 PRO A 44 82.86 -69.74 REMARK 500 19 LEU A 60 155.55 -38.48 REMARK 500 19 ASP A 70 -74.70 -40.61 REMARK 500 19 GLU A 84 127.24 -39.53 REMARK 500 19 PRO A 85 -178.44 -69.68 REMARK 500 19 ALA A 106 -73.03 -63.39 REMARK 500 19 SER A 118 -175.85 -58.12 REMARK 500 20 SER A 5 128.85 -172.46 REMARK 500 20 SER A 6 123.34 -170.97 REMARK 500 20 MET A 14 43.75 -98.09 REMARK 500 20 PRO A 24 -174.92 -69.73 REMARK 500 20 PRO A 28 99.38 -69.77 REMARK 500 20 GLN A 36 95.67 -42.73 REMARK 500 20 GLU A 38 107.87 -55.86 REMARK 500 20 VAL A 40 -58.69 -133.20 REMARK 500 20 ASP A 58 38.84 74.03 REMARK 500 20 GLU A 84 117.15 -36.79 REMARK 500 20 PRO A 120 -172.75 -69.67 REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSK002001303.1 RELATED DB: TARGETDB
DBREF 1WGO A 8 117 UNP Q96PQ0 SORC2_HUMAN 760 869
SEQADV 1WGO GLY A 1 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 2 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 3 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO GLY A 4 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 5 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 6 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO GLY A 7 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 118 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO GLY A 119 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO PRO A 120 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 121 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO SER A 122 UNP Q96PQ0 CLONING ARTIFACT SEQADV 1WGO GLY A 123 UNP Q96PQ0 CLONING ARTIFACT
SEQRES 1 A 123 GLY SER SER GLY SER SER GLY CYS GLU GLY GLY VAL ASP SEQRES 2 A 123 MET GLN GLN SER GLN VAL GLN LEU GLN CYS PRO LEU THR SEQRES 3 A 123 PRO PRO ARG GLY LEU GLN VAL SER ILE GLN GLY GLU ALA SEQRES 4 A 123 VAL ALA VAL ARG PRO GLY GLU ASP VAL LEU PHE VAL VAL SEQRES 5 A 123 ARG GLN GLU GLN GLY ASP VAL LEU THR THR LYS TYR GLN SEQRES 6 A 123 VAL ASP LEU GLY ASP GLY PHE LYS ALA MET TYR VAL ASN SEQRES 7 A 123 LEU THR LEU THR GLY GLU PRO ILE ARG HIS ARG TYR GLU SEQRES 8 A 123 SER PRO GLY ILE TYR ARG VAL SER VAL ARG ALA GLU ASN SEQRES 9 A 123 THR ALA GLY HIS ASP GLU ALA VAL LEU PHE VAL GLN VAL SEQRES 10 A 123 SER GLY PRO SER SER GLY
HELIX 1 1 ASN A 78 GLY A 83 1 6
SHEET 1 A 3 LEU A 31 ILE A 35 0 SHEET 2 A 3 VAL A 48 GLN A 54 -1 O VAL A 51 N SER A 34 SHEET 3 A 3 ILE A 86 HIS A 88 -1 O HIS A 88 N VAL A 48 SHEET 1 B 4 LYS A 73 VAL A 77 0 SHEET 2 B 4 LYS A 63 ASP A 67 -1 N TYR A 64 O TYR A 76 SHEET 3 B 4 TYR A 96 GLU A 103 -1 O SER A 99 N ASP A 67 SHEET 4 B 4 HIS A 108 VAL A 115 -1 O ASP A 109 N ALA A 102
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