PDB Short entry for 1IQ3 HEADER ENDOCYTOSIS/EXOCYTOSIS 06-JUN-01 1IQ3 TITLE SOLUTION STRUCTURE OF THE EPS15 HOMOLOGY DOMAIN OF A HUMAN POB1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RALBP1-INTERACTING PROTEIN (PARTNER OF RALBP1); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: EH DOMAIN(RESIDUES 126-228); 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS EF-HAND DOMAIN, POB1 EH DOMAIN, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 2 INITIATIVE, RSGI, STRUCTURAL GENOMICS, ENDOCYTOSIS-EXOCYTOSIS KEYWDS 3 COMPLEX EXPDTA SOLUTION NMR NUMMDL 18 AUTHOR S.KOSHIBA,T.KIGAWA,J.IWAHARA,A.KIKUCHI,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 6 27-DEC-23 1IQ3 1 REMARK REVDAT 5 23-FEB-22 1IQ3 1 REMARK LINK REVDAT 4 24-FEB-09 1IQ3 1 VERSN REVDAT 3 01-APR-03 1IQ3 1 JRNL REVDAT 2 14-JAN-03 1IQ3 1 REMARK REVDAT 1 27-JUN-01 1IQ3 0 JRNL AUTH S.KOSHIBA,T.KIGAWA,J.IWAHARA,A.KIKUCHI,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE EPS15 HOMOLOGY DOMAIN OF A HUMAN JRNL TITL 2 POB1 (PARTNER OF RALBP1). JRNL REF FEBS LETT. V. 442 138 1999 JRNL REFN ISSN 0014-5793 JRNL PMID 9928989 JRNL DOI 10.1016/S0014-5793(98)01644-5 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IQ3 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-JUN-01. REMARK 100 THE DEPOSITION ID IS D_1000005167. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 50MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM POB1 EH DOMAIN U-15N; 20MM REMARK 210 TRIS-HCL BUFFER, 50MM KCL, 5MM REMARK 210 DTT, 0.01% SODIUM AZIDE, 5MM REMARK 210 CACL2; 90% H2O,10% D2O; 2MM POB1 REMARK 210 EH DOMAIN U-13C,15N; 20MM TRIS- REMARK 210 HCL BUFFER, 50MM KCL, 5MM DTT, REMARK 210 0.01% SODIUM AZIDE, 10MM CACL2; REMARK 210 90% H2O,10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, NMRVIEW, X-PLOR 3.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 18 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: 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 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 LEU A 3 86.02 44.60 REMARK 500 1 ASP A 5 53.07 -172.16 REMARK 500 1 TYR A 9 72.13 -165.43 REMARK 500 1 PRO A 10 -158.51 -58.03 REMARK 500 1 ASP A 11 141.12 -171.09 REMARK 500 1 GLU A 12 -61.58 -172.92 REMARK 500 1 ILE A 16 -151.60 -177.84 REMARK 500 1 THR A 17 79.36 -176.77 REMARK 500 1 GLU A 18 12.97 59.01 REMARK 500 1 SER A 36 -81.34 -119.69 REMARK 500 1 SER A 37 -154.10 47.74 REMARK 500 1 LYS A 50 53.96 -159.59 REMARK 500 1 SER A 51 -48.65 -173.16 REMARK 500 1 LEU A 53 104.67 57.36 REMARK 500 1 SER A 54 179.58 52.02 REMARK 500 1 ILE A 55 95.05 48.14 REMARK 500 1 PRO A 56 93.75 -60.68 REMARK 500 1 ALA A 67 32.59 -145.42 REMARK 500 1 ASP A 68 27.36 -173.19 REMARK 500 1 CYS A 69 32.40 37.34 REMARK 500 1 THR A 74 170.12 -47.89 REMARK 500 1 GLU A 96 -159.86 -134.71 REMARK 500 1 PRO A 100 -179.80 -69.27 REMARK 500 1 THR A 101 74.23 169.45 REMARK 500 1 LEU A 102 -68.74 -164.23 REMARK 500 1 GLN A 103 58.44 -165.78 REMARK 500 1 VAL A 108 103.43 -57.62 REMARK 500 2 GLN A 4 103.19 53.54 REMARK 500 2 ASN A 6 -155.16 -151.05 REMARK 500 2 TYR A 9 79.80 61.09 REMARK 500 2 GLU A 12 -63.41 -167.27 REMARK 500 2 ILE A 16 -151.17 -128.14 REMARK 500 2 THR A 17 80.21 -178.31 REMARK 500 2 SER A 36 65.69 -107.43 REMARK 500 2 SER A 40 178.45 -59.59 REMARK 500 2 SER A 51 -49.95 -174.32 REMARK 500 2 LEU A 53 -92.85 45.25 REMARK 500 2 ILE A 55 93.54 55.91 REMARK 500 2 PRO A 56 103.98 -58.72 REMARK 500 2 ASP A 68 24.67 -168.27 REMARK 500 2 CYS A 69 32.94 38.09 REMARK 500 2 TYR A 92 79.49 47.84 REMARK 500 2 LEU A 94 129.50 60.91 REMARK 500 2 GLU A 96 -153.84 -101.86 REMARK 500 2 LEU A 98 121.64 58.30 REMARK 500 2 GLN A 103 126.88 64.62 REMARK 500 2 PRO A 104 85.17 -61.25 REMARK 500 2 PHE A 106 40.68 -94.86 REMARK 500 2 ILE A 107 -47.51 -156.99 REMARK 500 3 GLN A 4 -54.35 -168.58 REMARK 500 REMARK 500 THIS ENTRY HAS 435 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 1 ARG A 15 0.30 SIDE CHAIN REMARK 500 1 ARG A 21 0.20 SIDE CHAIN REMARK 500 1 ARG A 29 0.29 SIDE CHAIN REMARK 500 2 ARG A 15 0.32 SIDE CHAIN REMARK 500 2 ARG A 21 0.30 SIDE CHAIN REMARK 500 2 ARG A 29 0.22 SIDE CHAIN REMARK 500 2 ARG A 88 0.13 SIDE CHAIN REMARK 500 3 ARG A 15 0.31 SIDE CHAIN REMARK 500 3 ARG A 21 0.21 SIDE CHAIN REMARK 500 3 ARG A 29 0.29 SIDE CHAIN REMARK 500 3 ARG A 88 0.27 SIDE CHAIN REMARK 500 4 ARG A 15 0.24 SIDE CHAIN REMARK 500 4 ARG A 21 0.20 SIDE CHAIN REMARK 500 4 ARG A 29 0.08 SIDE CHAIN REMARK 500 4 ARG A 88 0.24 SIDE CHAIN REMARK 500 5 ARG A 15 0.29 SIDE CHAIN REMARK 500 5 ARG A 21 0.18 SIDE CHAIN REMARK 500 5 ARG A 29 0.29 SIDE CHAIN REMARK 500 6 ARG A 15 0.19 SIDE CHAIN REMARK 500 6 ARG A 21 0.27 SIDE CHAIN REMARK 500 6 ARG A 29 0.32 SIDE CHAIN REMARK 500 6 ARG A 88 0.27 SIDE CHAIN REMARK 500 7 ARG A 15 0.11 SIDE CHAIN REMARK 500 7 ARG A 21 0.31 SIDE CHAIN REMARK 500 7 ARG A 29 0.30 SIDE CHAIN REMARK 500 8 ARG A 15 0.22 SIDE CHAIN REMARK 500 8 ARG A 21 0.20 SIDE CHAIN REMARK 500 8 ARG A 29 0.27 SIDE CHAIN REMARK 500 8 ARG A 88 0.32 SIDE CHAIN REMARK 500 9 ARG A 15 0.12 SIDE CHAIN REMARK 500 9 ARG A 21 0.21 SIDE CHAIN REMARK 500 9 ARG A 29 0.31 SIDE CHAIN REMARK 500 9 ARG A 88 0.27 SIDE CHAIN REMARK 500 10 ARG A 15 0.29 SIDE CHAIN REMARK 500 10 ARG A 21 0.31 SIDE CHAIN REMARK 500 10 ARG A 29 0.12 SIDE CHAIN REMARK 500 10 ARG A 88 0.22 SIDE CHAIN REMARK 500 11 ARG A 15 0.23 SIDE CHAIN REMARK 500 11 ARG A 21 0.28 SIDE CHAIN REMARK 500 11 ARG A 29 0.29 SIDE CHAIN REMARK 500 11 ARG A 88 0.21 SIDE CHAIN REMARK 500 12 ARG A 15 0.24 SIDE CHAIN REMARK 500 12 ARG A 21 0.28 SIDE CHAIN REMARK 500 12 ARG A 29 0.19 SIDE CHAIN REMARK 500 12 ARG A 88 0.26 SIDE CHAIN REMARK 500 13 ARG A 15 0.30 SIDE CHAIN REMARK 500 13 ARG A 21 0.24 SIDE CHAIN REMARK 500 13 ARG A 29 0.28 SIDE CHAIN REMARK 500 13 ARG A 88 0.11 SIDE CHAIN REMARK 500 14 ARG A 15 0.30 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 68 PLANE DEVIATIONS. 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 A 111 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 66 OD1 REMARK 620 2 ALA A 67 N 60.4 REMARK 620 3 ASP A 68 OD1 58.0 68.4 REMARK 620 4 ASP A 70 OD1 49.3 101.1 47.9 REMARK 620 5 ALA A 72 O 89.3 148.0 105.8 60.0 REMARK 620 6 GLU A 77 OE1 136.3 106.0 161.1 148.3 88.4 REMARK 620 7 GLU A 77 OE2 171.6 112.5 116.1 132.7 98.4 48.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 111 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: TRT001000213.1 RELATED DB: TARGETDB DBREF 1IQ3 A 3 105 UNP Q8NFH8 REPS2_HUMAN 126 228 SEQADV 1IQ3 GLY A 1 UNP Q8NFH8 SEE REMARK 999 SEQADV 1IQ3 SER A 2 UNP Q8NFH8 SEE REMARK 999 SEQADV 1IQ3 PHE A 106 UNP Q8NFH8 SEE REMARK 999 SEQADV 1IQ3 ILE A 107 UNP Q8NFH8 SEE REMARK 999 SEQADV 1IQ3 VAL A 108 UNP Q8NFH8 SEE REMARK 999 SEQADV 1IQ3 THR A 109 UNP Q8NFH8 SEE REMARK 999 SEQADV 1IQ3 ASP A 110 UNP Q8NFH8 SEE REMARK 999 SEQRES 1 A 110 GLY SER LEU GLN ASP ASN SER SER TYR PRO ASP GLU PRO SEQRES 2 A 110 TRP ARG ILE THR GLU GLU GLN ARG GLU TYR TYR VAL ASN SEQRES 3 A 110 GLN PHE ARG SER LEU GLN PRO ASP PRO SER SER PHE ILE SEQRES 4 A 110 SER GLY SER VAL ALA LYS ASN PHE PHE THR LYS SER LYS SEQRES 5 A 110 LEU SER ILE PRO GLU LEU SER TYR ILE TRP GLU LEU SER SEQRES 6 A 110 ASP ALA ASP CYS ASP GLY ALA LEU THR LEU PRO GLU PHE SEQRES 7 A 110 CYS ALA ALA PHE HIS LEU ILE VAL ALA ARG LYS ASN GLY SEQRES 8 A 110 TYR PRO LEU PRO GLU GLY LEU PRO PRO THR LEU GLN PRO SEQRES 9 A 110 GLU PHE ILE VAL THR ASP HET CA A 111 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ HELIX 1 1 GLU A 18 LEU A 31 1 14 HELIX 2 2 GLY A 41 THR A 49 1 9 HELIX 3 3 GLU A 57 SER A 65 1 9 HELIX 4 4 LEU A 75 ASN A 90 1 16 SHEET 1 A 2 PHE A 38 SER A 40 0 SHEET 2 A 2 ALA A 72 THR A 74 -1 N LEU A 73 O ILE A 39 LINK OD1 ASP A 66 CA CA A 111 1555 1555 2.70 LINK N ALA A 67 CA CA A 111 1555 1555 3.34 LINK OD1 ASP A 68 CA CA A 111 1555 1555 2.91 LINK OD1 ASP A 70 CA CA A 111 1555 1555 2.88 LINK O ALA A 72 CA CA A 111 1555 1555 2.77 LINK OE1 GLU A 77 CA CA A 111 1555 1555 2.59 LINK OE2 GLU A 77 CA CA A 111 1555 1555 2.70 SITE 1 AC1 7 ASP A 66 ALA A 67 ASP A 68 ASP A 70 SITE 2 AC1 7 ALA A 72 LEU A 73 GLU A 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