PDB Short entry for 2H4D HEADER TRANSPORT PROTEIN 24-MAY-06 2H4D TITLE NUCLEAR PORE COMPLEX P62 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPORIN 62KDA; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NUP62 PROTEIN, NUCLEAR PORE COMPLEX P62 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 GENUS: NUP62 KEYWDS HELIX-TURN- BETA STRAND EXPDTA THEORETICAL MODEL AUTHOR L.PRABAKAR,K.G.RAMESH REVDAT 1 29-MAY-07 2H4D 0 JRNL AUTH L.PRABAKAR,K.G.RAMESH JRNL TITL EFFECT OF OXALATE ON TRANSCRIPTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : GROMOS GROMOS 96 IMPLEMENTATION OF SPDBV REMARK 3 AUTHORS : W.F. VAN GUNSTEREN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2H4D COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-05-25) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-MAY-2006. REMARK 100 THE RCSB ID CODE IS RCSB037914. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THIS MODEL WAS PRODUCED BY MODELLER MOD8V1 REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ALA A 107 N ALA A 107 CA 0.086 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 106 CA - C - O ANGL. DEV. =-23.5 DEGREES REMARK 500 SER A 112 C - N - CA ANGL. DEV. = 18.8 DEGREES REMARK 500 SER A 374 N - CA - C ANGL. DEV. = 18.4 DEGREES REMARK 500 LEU A 375 N - CA - C ANGL. DEV. = 19.4 DEGREES REMARK 500 ARG A 377 CB - CA - C ANGL. DEV. =-20.1 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 ALA A 104 -104.62 169.13 REMARK 500 THR A 105 169.10 69.44 REMARK 500 GLN A 449 130.38 73.32 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 14 GLY A 15 -149.23 REMARK 500 GLY A 15 PHE A 16 140.79 REMARK 500 GLN A 353 GLN A 354 -146.25 REMARK 500 HIS A 376 ARG A 377 142.63 REMARK 500 ASN A 439 ILE A 440 148.83 DBREF 2H4D A 1 522 UNP Q6GTM2 Q6GTM2_HUMAN 1 522 SEQRES 1 A 522 MET SER GLY PHE ASN PHE GLY GLY THR GLY ALA PRO THR SEQRES 2 A 522 GLY GLY PHE THR PHE GLY THR ALA LYS THR ALA THR THR SEQRES 3 A 522 THR PRO ALA THR GLY PHE SER PHE SER THR SER GLY THR SEQRES 4 A 522 GLY GLY PHE ASN PHE GLY ALA PRO PHE GLN PRO ALA THR SEQRES 5 A 522 SER THR PRO SER THR GLY LEU PHE SER LEU ALA THR GLN SEQRES 6 A 522 THR PRO ALA THR GLN THR THR GLY PHE THR PHE GLY THR SEQRES 7 A 522 ALA THR LEU ALA SER GLY GLY THR GLY PHE SER LEU GLY SEQRES 8 A 522 ILE GLY ALA SER LYS LEU ASN LEU SER ASN THR ALA ALA SEQRES 9 A 522 THR PRO ALA MET ALA ASN PRO SER GLY PHE GLY LEU GLY SEQRES 10 A 522 SER SER ASN LEU THR ASN ALA ILE SER SER THR VAL THR SEQRES 11 A 522 SER SER GLN GLY THR ALA PRO THR GLY PHE VAL PHE GLY SEQRES 12 A 522 PRO SER THR THR SER VAL ALA PRO ALA THR THR SER GLY SEQRES 13 A 522 GLY PHE SER PHE THR GLY GLY SER THR ALA GLN PRO SER SEQRES 14 A 522 GLY PHE ASN ILE GLY SER ALA GLY ASN SER ALA GLN PRO SEQRES 15 A 522 THR ALA PRO ALA THR LEU PRO PHE THR PRO ALA THR PRO SEQRES 16 A 522 ALA ALA THR THR ALA GLY ALA THR GLN PRO ALA ALA PRO SEQRES 17 A 522 THR PRO THR ALA THR ILE THR SER THR GLY PRO SER LEU SEQRES 18 A 522 PHE ALA SER ILE ALA THR ALA PRO THR SER SER ALA THR SEQRES 19 A 522 THR GLY LEU SER LEU CYS THR PRO VAL THR THR ALA GLY SEQRES 20 A 522 ALA PRO THR ALA GLY THR GLN GLY PHE SER LEU LYS ALA SEQRES 21 A 522 PRO GLY ALA ALA SER GLY THR SER THR THR THR SER THR SEQRES 22 A 522 ALA ALA THR ALA THR ALA THR THR THR SER SER SER SER SEQRES 23 A 522 THR THR GLY PHE ALA LEU ASN LEU LYS PRO LEU ALA PRO SEQRES 24 A 522 ALA GLY ILE PRO SER ASN THR ALA ALA ALA VAL THR ALA SEQRES 25 A 522 PRO PRO GLY PRO GLY ALA ALA ALA GLY ALA ALA ALA SER SEQRES 26 A 522 SER ALA MET THR TYR ALA GLN LEU GLU SER LEU ILE ASN SEQRES 27 A 522 LYS TRP SER LEU GLU LEU GLU ASP GLN GLU ARG HIS PHE SEQRES 28 A 522 LEU GLN GLN ALA THR GLN VAL ASN ALA TRP ASP ARG THR SEQRES 29 A 522 LEU ILE GLU ASN GLY GLU LYS ILE THR SER LEU HIS ARG SEQRES 30 A 522 GLU VAL GLU LYS VAL LYS LEU ASP GLN LYS ARG LEU ASP SEQRES 31 A 522 GLN GLU LEU ASP PHE ILE LEU SER GLN GLN LYS GLU LEU SEQRES 32 A 522 GLU ASP LEU LEU SER PRO LEU GLU GLU LEU VAL LYS GLU SEQRES 33 A 522 GLN SER GLY THR ILE TYR LEU GLN HIS ALA ASP GLU GLU SEQRES 34 A 522 ARG GLU LYS THR TYR LYS LEU ALA GLU ASN ILE ASP ALA SEQRES 35 A 522 GLN LEU LYS ARG MET ALA GLN ASP LEU LYS ASP ILE ILE SEQRES 36 A 522 GLU HIS LEU ASN THR SER GLY ALA PRO ALA ASP THR SER SEQRES 37 A 522 ASP PRO LEU GLN GLN ILE CYS LYS ILE LEU ASN ALA HIS SEQRES 38 A 522 MET ASP SER LEU GLN TRP ILE ASP GLN ASN SER ALA LEU SEQRES 39 A 522 LEU GLN ARG LYS VAL GLU GLU VAL THR LYS VAL CYS GLU SEQRES 40 A 522 GLY ARG ARG LYS GLU GLN GLU ARG SER PHE ARG ILE THR SEQRES 41 A 522 PHE ASP HELIX 1 1 GLY A 15 GLY A 19 1 5 HELIX 2 2 ALA A 21 THR A 27 1 7 HELIX 3 3 GLY A 41 GLN A 49 1 9 HELIX 4 4 THR A 52 GLN A 70 1 19 HELIX 5 5 GLN A 70 GLY A 84 1 15 HELIX 6 6 PHE A 88 ASN A 101 1 14 HELIX 7 7 ALA A 124 ALA A 136 1 13 HELIX 8 8 SER A 145 GLY A 162 1 18 HELIX 9 9 THR A 165 GLY A 177 1 13 HELIX 10 10 PRO A 182 THR A 199 1 18 HELIX 11 11 THR A 203 ALA A 206 5 4 HELIX 12 12 ALA A 207 GLY A 218 1 12 HELIX 13 13 ALA A 226 CYS A 240 1 15 HELIX 14 14 VAL A 243 ALA A 248 1 6 HELIX 15 15 PRO A 249 SER A 265 1 17 HELIX 16 16 SER A 268 SER A 286 1 19 HELIX 17 17 PHE A 290 LYS A 295 1 6 HELIX 18 18 GLY A 301 ALA A 312 1 12 HELIX 19 19 GLY A 321 LEU A 352 1 32 HELIX 20 20 GLN A 353 ASN A 359 1 7 HELIX 21 21 ASN A 359 GLU A 367 1 9 HELIX 22 22 HIS A 376 ASP A 390 1 15 HELIX 23 23 GLU A 392 GLN A 417 1 26 HELIX 24 24 ALA A 426 ASN A 439 1 14 HELIX 25 25 GLU A 456 ALA A 463 1 8 HELIX 26 26 ALA A 463 SER A 468 1 6 HELIX 27 27 ASP A 469 GLN A 490 1 22 HELIX 28 28 LEU A 494 GLY A 508 1 15 HELIX 29 29 ARG A 509 SER A 516 1 8 SHEET 1 A 2 THR A 20 THR A 20 0 SHEET 2 A 2 LEU A 121 ASN A 123 1 O THR A 122 N THR A 20 CISPEP 1 GLY A 143 PRO A 144 0 -10.19 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