PDB Short entry for 2KSP HEADER PROTEIN BINDING 11-JAN-10 2KSP TITLE MECHANISM FOR THE SELECTIVE INTERACTION OF C-TERMINAL EH-DOMAIN TITLE 2 PROTEINS WITH SPECIFIC NPF-CONTAINING PARTNERS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EH DOMAIN-CONTAINING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN (UNP RESIDUES 435-534); COMPND 5 SYNONYM: TESTILIN, HPAST1; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: MICAL L1 LIKE PEPTIDE; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: MOLECULE INTERACTING WITH RAB13, MIRAB13; COMPND 11 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: EHD1, PAST, PAST1, CDABP0131; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX6P-2; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES KEYWDS EHD1, ENDOCYTIC RECYCLING, PROTEIN-PROTEIN INTERACTIONS, PROTEIN KEYWDS 2 BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR F.KIEKEN,M.SHARMA,M.JOVIC,S.S.GIRIDHARAN,N.NASLAVSKY,S.CAPLAN, AUTHOR 2 P.L.SORGEN REVDAT 3 26-FEB-20 2KSP 1 REMARK SEQADV REVDAT 2 05-MAY-10 2KSP 1 JRNL REVDAT 1 26-JAN-10 2KSP 0 JRNL AUTH F.KIEKEN,M.SHARMA,M.JOVIC,S.S.GIRIDHARAN,N.NASLAVSKY, JRNL AUTH 2 S.CAPLAN,P.L.SORGEN JRNL TITL MECHANISM FOR THE SELECTIVE INTERACTION OF C-TERMINAL EPS15 JRNL TITL 2 HOMOLOGY DOMAIN PROTEINS WITH SPECIFIC JRNL TITL 3 ASN-PRO-PHE-CONTAINING PARTNERS. JRNL REF J.BIOL.CHEM. V. 285 8687 2010 JRNL REFN ISSN 0021-9258 JRNL PMID 20106972 JRNL DOI 10.1074/JBC.M109.045666 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRVIEW, ARIA 1.2 REMARK 3 AUTHORS : JOHNSON, ONE MOON SCIENTIFIC (NMRVIEW) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000101526. 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 : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.6 MM [U-99% 13C; U-99% 15N] EH REMARK 210 DOMAIN OF EHD1, 2 MM MICAL L1 REMARK 210 LIKE PEPTIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 2D 13CFILTERED- REMARK 210 13CFILTEREDNOESY; 2D 13C- REMARK 210 FILTERED-15N EDITEDNOESY; 2D 15N REMARK 210 FILTERED NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, PROCHECKNMR, VNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 OE2 GLU A 104 HZ2 LYS A 135 1.56 REMARK 500 HZ1 LYS A 91 OE1 GLU B 152 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 8 TYR A 53 CE1 TYR A 53 CZ 0.091 REMARK 500 8 TYR A 53 CZ TYR A 53 CE2 -0.092 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 SER A 61 84.86 68.76 REMARK 500 1 GLU B 154 148.93 72.22 REMARK 500 1 GLU B 155 -73.07 -105.47 REMARK 500 2 VAL A 45 5.72 -69.87 REMARK 500 2 SER A 61 93.09 70.07 REMARK 500 2 PRO A 123 24.30 -73.07 REMARK 500 2 SER B 145 98.58 -66.70 REMARK 500 2 PRO B 147 23.58 -73.29 REMARK 500 2 GLU B 153 -72.86 -75.22 REMARK 500 2 GLU B 154 -100.41 45.82 REMARK 500 3 SER A 61 89.32 69.29 REMARK 500 3 ASN A 64 23.71 49.48 REMARK 500 3 LYS B 146 79.54 58.58 REMARK 500 3 GLU B 154 -154.30 57.37 REMARK 500 3 GLU B 156 58.79 -141.16 REMARK 500 4 SER A 61 86.15 64.71 REMARK 500 4 LYS A 97 72.48 60.66 REMARK 500 4 PRO A 133 11.28 -67.85 REMARK 500 4 PRO B 147 -167.21 -78.11 REMARK 500 4 GLU B 154 174.46 73.17 REMARK 500 4 GLU B 155 151.18 72.20 REMARK 500 4 GLU B 156 107.14 69.30 REMARK 500 5 SER A 61 94.05 67.91 REMARK 500 5 LYS A 97 73.46 61.01 REMARK 500 5 LEU A 130 -35.37 -131.71 REMARK 500 5 GLU B 144 -75.88 -90.44 REMARK 500 5 SER B 145 -97.66 -118.60 REMARK 500 5 LYS B 146 72.40 52.16 REMARK 500 5 GLU B 154 151.43 68.85 REMARK 500 5 GLU B 155 -68.21 -99.34 REMARK 500 6 SER A 61 92.03 68.00 REMARK 500 6 LYS A 97 74.48 66.15 REMARK 500 6 GLU B 154 -79.69 65.05 REMARK 500 7 SER A 61 90.10 66.51 REMARK 500 7 LYS A 97 72.07 54.74 REMARK 500 7 PRO B 147 -79.44 -84.34 REMARK 500 7 TYR B 148 -36.83 -139.13 REMARK 500 7 GLU B 154 149.66 68.92 REMARK 500 7 GLU B 155 -165.04 -113.73 REMARK 500 8 SER A 61 88.69 65.06 REMARK 500 8 LYS A 97 76.40 73.45 REMARK 500 8 SER B 145 -166.04 54.19 REMARK 500 8 LYS B 146 92.79 63.27 REMARK 500 8 GLU B 154 -175.56 67.25 REMARK 500 9 SER A 61 84.70 59.18 REMARK 500 9 LYS A 97 73.64 56.17 REMARK 500 9 PRO B 147 -179.74 -69.56 REMARK 500 9 GLU B 154 111.40 75.30 REMARK 500 9 GLU B 155 -72.56 -147.45 REMARK 500 9 GLU B 156 -74.69 -112.84 REMARK 500 REMARK 500 THIS ENTRY HAS 54 RAMACHANDRAN OUTLIERS. 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 141 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 100 O REMARK 620 2 GLU A 105 OE2 142.2 REMARK 620 N 1 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 141 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16671 RELATED DB: BMRB DBREF 2KSP A 40 139 UNP Q9H4M9 EHD1_HUMAN 435 534 DBREF 2KSP B 143 157 UNP Q8N3F8 MILK1_HUMAN 419 433 SEQADV 2KSP GLY A 35 UNP Q9H4M9 EXPRESSION TAG SEQADV 2KSP PRO A 36 UNP Q9H4M9 EXPRESSION TAG SEQADV 2KSP LEU A 37 UNP Q9H4M9 EXPRESSION TAG SEQADV 2KSP GLY A 38 UNP Q9H4M9 EXPRESSION TAG SEQADV 2KSP SER A 39 UNP Q9H4M9 EXPRESSION TAG SEQRES 1 A 105 GLY PRO LEU GLY SER ASP ASP VAL GLU TRP VAL VAL GLY SEQRES 2 A 105 LYS ASP LYS PRO THR TYR ASP GLU ILE PHE TYR THR LEU SEQRES 3 A 105 SER PRO VAL ASN GLY LYS ILE THR GLY ALA ASN ALA LYS SEQRES 4 A 105 LYS GLU MET VAL LYS SER LYS LEU PRO ASN THR VAL LEU SEQRES 5 A 105 GLY LYS ILE TRP LYS LEU ALA ASP VAL ASP LYS ASP GLY SEQRES 6 A 105 LEU LEU ASP ASP GLU GLU PHE ALA LEU ALA ASN HIS LEU SEQRES 7 A 105 ILE LYS VAL LYS LEU GLU GLY HIS GLU LEU PRO ALA ASP SEQRES 8 A 105 LEU PRO PRO HIS LEU VAL PRO PRO SER LYS ARG ARG HIS SEQRES 9 A 105 GLU SEQRES 1 B 15 LEU GLU SER LYS PRO TYR ASN PRO PHE GLU GLU GLU GLU SEQRES 2 B 15 GLU ASP HET CA A 141 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ HELIX 1 1 VAL A 45 LEU A 60 1 16 HELIX 2 2 PRO A 62 LYS A 66 5 5 HELIX 3 3 THR A 68 SER A 79 1 12 HELIX 4 4 PRO A 82 ASP A 94 1 13 HELIX 5 5 ASP A 102 GLU A 118 1 17 HELIX 6 6 PRO A 132 ARG A 136 5 5 LINK O LEU A 100 CA CA A 141 1555 1555 2.02 LINK OE2 GLU A 105 CA CA A 141 1555 1555 2.08 SITE 1 AC1 5 ASP A 94 ASP A 96 ASP A 98 LEU A 100 SITE 2 AC1 5 GLU A 105 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