HEADER TRANSFERASE 16-JUN-07 2Z4F
TITLE SOLUTION STRUCTURE OF THE DISCOIDIN DOMAIN OF DDR2
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: DISCOIDIN DOMAIN-CONTAINING RECEPTOR 2;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: F5/8 TYPE C, DISCOIDIN DOMAIN, RESIDUES 26-186;
COMPND 5 SYNONYM: DISCOIDIN DOMAIN RECEPTOR 2, RECEPTOR PROTEIN-TYROSINE
COMPND 6 KINASE TKT, TYROSINE-PROTEIN KINASE TYRO10, NEUROTROPHIC TYROSINE
COMPND 7 KINASE, RECEPTOR-RELATED 3, CD167B ANTIGEN;
COMPND 8 EC: 2.7.10.1;
COMPND 9 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: DDR2;
SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922
KEYWDS BETA BARREL, TRANSFERASE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR O.ICHIKAWA,M.OSAWA,N.NISHIDA,N.GOSHIMA,N.NOMURA,I.SHIMADA
REVDAT 4 16-MAR-22 2Z4F 1 REMARK SEQADV
REVDAT 3 24-FEB-09 2Z4F 1 VERSN
REVDAT 2 16-OCT-07 2Z4F 1 JRNL
REVDAT 1 04-SEP-07 2Z4F 0
JRNL AUTH O.ICHIKAWA,M.OSAWA,N.NISHIDA,N.GOSHIMA,N.NOMURA,I.SHIMADA
JRNL TITL STRUCTURAL BASIS OF THE COLLAGEN-BINDING MODE OF DISCOIDIN
JRNL TITL 2 DOMAIN RECEPTOR 2
JRNL REF EMBO J. V. 26 4168 2007
JRNL REFN ISSN 0261-4189
JRNL PMID 17703188
JRNL DOI 10.1038/SJ.EMBOJ.7601833
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.1
REMARK 3 AUTHORS : GUNTERT, P. ET AL.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2Z4F COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JUN-07.
REMARK 100 THE DEPOSITION ID IS D_1000027507.
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 : 0.1M
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 0.4MM DDR2 U-15N,13C; 10MM
REMARK 210 PHOSPHATE BUFFER; 100MM NACL; 95%
REMARK 210 H2O, 5% D2O; 0.4MM DDR2 U-15N,
REMARK 210 13C; 10MM PHOSPHATE BUFFER;
REMARK 210 100MM NACL; 100% D2O; 0.4MM DDR2
REMARK 210 U-15N; 10MM PHOSPHATE BUFFER;
REMARK 210 100MM NACL; 95% H2O, 5% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_13C
REMARK 210 -SEPARATED_NOESY; HNHA; 3D_15N-
REMARK 210 SEPARATED_NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CYANA 2.1
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 200
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: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR
REMARK 210 SPECTROSCOPY.
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 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 GLU A 22
REMARK 465 ALA A 23
REMARK 465 GLU A 24
REMARK 465 PHE A 25
REMARK 465 GLY A 187
REMARK 465 SER A 188
REMARK 465 GLY A 189
REMARK 465 SER A 190
REMARK 465 ILE A 191
REMARK 465 GLU A 192
REMARK 465 GLY A 193
REMARK 465 ARG A 194
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 PRO A 42 -170.08 -69.74
REMARK 500 1 SER A 49 42.97 -94.95
REMARK 500 1 SER A 50 47.97 -178.54
REMARK 500 1 SER A 53 -169.51 -129.13
REMARK 500 1 LEU A 63 -75.53 -59.04
REMARK 500 1 ASP A 64 53.80 -94.22
REMARK 500 1 GLU A 66 117.41 -165.43
REMARK 500 1 PRO A 74 -166.93 -69.75
REMARK 500 1 PHE A 86 -174.41 -179.83
REMARK 500 1 LEU A 94 103.89 -50.12
REMARK 500 1 HIS A 106 124.00 -174.39
REMARK 500 1 TYR A 118 140.97 -174.85
REMARK 500 1 PRO A 158 -169.89 -69.79
REMARK 500 1 ALA A 161 -172.07 -173.47
REMARK 500 2 PRO A 42 -170.66 -69.72
REMARK 500 2 SER A 50 59.38 -178.12
REMARK 500 2 TRP A 52 -54.07 -125.22
REMARK 500 2 GLU A 66 111.08 -160.90
REMARK 500 2 PRO A 74 -170.46 -69.72
REMARK 500 2 PHE A 86 -175.21 -179.94
REMARK 500 2 HIS A 110 -57.53 -127.49
REMARK 500 2 TYR A 118 134.91 -174.51
REMARK 500 2 ASP A 125 -71.19 -79.34
REMARK 500 2 ASN A 144 133.54 -174.37
REMARK 500 2 ASN A 146 67.91 63.32
REMARK 500 2 TYR A 148 -55.33 -125.57
REMARK 500 2 PRO A 158 -169.56 -69.74
REMARK 500 3 PRO A 42 -170.79 -69.78
REMARK 500 3 SER A 49 39.11 -97.83
REMARK 500 3 SER A 50 50.22 -177.51
REMARK 500 3 THR A 56 32.15 -150.04
REMARK 500 3 PRO A 74 -169.32 -69.76
REMARK 500 3 ASP A 82 79.07 -106.50
REMARK 500 3 PHE A 86 -175.64 -179.61
REMARK 500 3 LEU A 94 103.83 -51.38
REMARK 500 3 HIS A 95 -169.62 -128.41
REMARK 500 3 PHE A 114 -169.82 -173.20
REMARK 500 3 TYR A 148 -39.64 -132.04
REMARK 500 3 PRO A 158 -168.58 -69.75
REMARK 500 3 ALA A 161 -176.02 -179.00
REMARK 500 3 HIS A 172 -176.19 -179.64
REMARK 500 4 PRO A 33 -178.26 -69.78
REMARK 500 4 PRO A 42 -171.23 -69.75
REMARK 500 4 SER A 50 80.36 177.83
REMARK 500 4 PRO A 74 -168.89 -69.73
REMARK 500 4 ASP A 81 -65.48 -101.09
REMARK 500 4 PHE A 86 -173.88 -179.74
REMARK 500 4 THR A 102 116.90 -162.95
REMARK 500 4 TYR A 118 139.57 -174.69
REMARK 500 4 SER A 123 149.25 -176.22
REMARK 500
REMARK 500 THIS ENTRY HAS 306 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
DBREF 2Z4F A 26 186 UNP Q16832 DDR2_HUMAN 26 186
SEQADV 2Z4F GLU A 22 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F ALA A 23 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F GLU A 24 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F PHE A 25 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F GLY A 187 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F SER A 188 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F GLY A 189 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F SER A 190 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F ILE A 191 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F GLU A 192 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F GLY A 193 UNP Q16832 EXPRESSION TAG
SEQADV 2Z4F ARG A 194 UNP Q16832 EXPRESSION TAG
SEQRES 1 A 173 GLU ALA GLU PHE ASN PRO ALA ILE CYS ARG TYR PRO LEU
SEQRES 2 A 173 GLY MET SER GLY GLY GLN ILE PRO ASP GLU ASP ILE THR
SEQRES 3 A 173 ALA SER SER GLN TRP SER GLU SER THR ALA ALA LYS TYR
SEQRES 4 A 173 GLY ARG LEU ASP SER GLU GLU GLY ASP GLY ALA TRP CYS
SEQRES 5 A 173 PRO GLU ILE PRO VAL GLU PRO ASP ASP LEU LYS GLU PHE
SEQRES 6 A 173 LEU GLN ILE ASP LEU HIS THR LEU HIS PHE ILE THR LEU
SEQRES 7 A 173 VAL GLY THR GLN GLY ARG HIS ALA GLY GLY HIS GLY ILE
SEQRES 8 A 173 GLU PHE ALA PRO MET TYR LYS ILE ASN TYR SER ARG ASP
SEQRES 9 A 173 GLY THR ARG TRP ILE SER TRP ARG ASN ARG HIS GLY LYS
SEQRES 10 A 173 GLN VAL LEU ASP GLY ASN SER ASN PRO TYR ASP ILE PHE
SEQRES 11 A 173 LEU LYS ASP LEU GLU PRO PRO ILE VAL ALA ARG PHE VAL
SEQRES 12 A 173 ARG PHE ILE PRO VAL THR ASP HIS SER MET ASN VAL CYS
SEQRES 13 A 173 MET ARG VAL GLU LEU TYR GLY CYS VAL GLY SER GLY SER
SEQRES 14 A 173 ILE GLU GLY ARG
SHEET 1 A 5 ILE A 46 SER A 49 0
SHEET 2 A 5 PHE A 86 GLY A 104 -1 O GLN A 88 N THR A 47
SHEET 3 A 5 PHE A 151 VAL A 169 -1 O ILE A 159 N ILE A 97
SHEET 4 A 5 MET A 117 SER A 123 -1 N ASN A 121 O ARG A 165
SHEET 5 A 5 VAL A 140 ASP A 142 -1 O LEU A 141 N TYR A 118
SHEET 1 B 5 ILE A 130 SER A 131 0
SHEET 2 B 5 MET A 117 SER A 123 -1 N TYR A 122 O ILE A 130
SHEET 3 B 5 PHE A 151 VAL A 169 -1 O ARG A 165 N ASN A 121
SHEET 4 B 5 PHE A 86 GLY A 104 -1 N ILE A 97 O ILE A 159
SHEET 5 B 5 MET A 178 CYS A 185 -1 O TYR A 183 N LEU A 99
SSBOND 1 CYS A 30 CYS A 185 1555 1555 2.01
SSBOND 2 CYS A 73 CYS A 177 1555 1555 1.95
CISPEP 1 GLU A 156 PRO A 157 1 0.05
CISPEP 2 GLU A 156 PRO A 157 2 -0.03
CISPEP 3 GLU A 156 PRO A 157 3 0.02
CISPEP 4 GLU A 156 PRO A 157 4 0.01
CISPEP 5 GLU A 156 PRO A 157 5 0.08
CISPEP 6 GLU A 156 PRO A 157 6 -0.05
CISPEP 7 GLU A 156 PRO A 157 7 -0.06
CISPEP 8 GLU A 156 PRO A 157 8 0.04
CISPEP 9 GLU A 156 PRO A 157 9 0.02
CISPEP 10 GLU A 156 PRO A 157 10 0.00
CISPEP 11 GLU A 156 PRO A 157 11 -0.01
CISPEP 12 GLU A 156 PRO A 157 12 0.05
CISPEP 13 GLU A 156 PRO A 157 13 -0.09
CISPEP 14 GLU A 156 PRO A 157 14 0.12
CISPEP 15 GLU A 156 PRO A 157 15 0.09
CISPEP 16 GLU A 156 PRO A 157 16 0.01
CISPEP 17 GLU A 156 PRO A 157 17 -0.03
CISPEP 18 GLU A 156 PRO A 157 18 0.02
CISPEP 19 GLU A 156 PRO A 157 19 0.02
CISPEP 20 GLU A 156 PRO A 157 20 -0.01
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
MODEL 1
(ATOM LINES ARE NOT SHOWN.)
END
