HEADER CELL ADHESION 17-APR-02 1LH9 TITLE THEORETICAL MODEL OF THE BETA6 INTEGRIN CAVEAT 1LH9 CHIRALITY ERROR AT THE CA CENTER OF HIS A 398. COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTEGRIN BETA-6; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN KEYWDS CELL ADHESION EXPDTA THEORETICAL MODEL AUTHOR S.RAMA DEVI,S.TAJNE,P.APARNA REVDAT 1 15-MAY-02 1LH9 0 JRNL AUTH S.RAMA DEVI,S.TAJNE,P.APARNA JRNL TITL THEORETICAL MODEL OF BETA6 INTEGRIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NULL REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LH9 COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-APR-2002. REMARK 100 THE RCSB ID CODE IS RCSB015945. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THIS MODEL IS BASED UPON THE COORDINATES OF:PDB ENTRY REMARK 220 1JV2/CELL ADHESION/28-AUG-01/CRYSTAL STRUCTURE OF THE REMARK 220 EXTRACELLULAR SEGMENT OF INTEGRIN ALPHAVBETA3/X-RAY REMARK 220 DIFFRACTION/RESOLUTION. 3.10 ANGSTROMS. 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: 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 REMARK 500 NH2 ARG A 24 CG TYR A 61 1.82 REMARK 500 NH2 ARG A 24 CD1 TYR A 61 1.83 REMARK 500 CZ ARG A 24 CG TYR A 61 1.98 REMARK 500 CZ ARG A 24 CD1 TYR A 61 2.00 REMARK 500 O GLU A 300 OE2 GLU A 304 2.10 REMARK 500 O CYS A 449 OE1 GLN A 451 2.12 REMARK 500 NH1 ARG A 24 CG TYR A 61 2.13 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 ARG A 24 CA ARG A 24 CB -0.277 REMARK 500 ARG A 24 CG ARG A 24 CD -0.267 REMARK 500 ARG A 24 CD ARG A 24 NE -0.248 REMARK 500 ARG A 24 NE ARG A 24 CZ -0.341 REMARK 500 ARG A 24 CZ ARG A 24 NH1 0.427 REMARK 500 ARG A 24 CZ ARG A 24 NH2 0.740 REMARK 500 LYS A 26 CB LYS A 26 CG -0.247 REMARK 500 LYS A 26 CE LYS A 26 NZ -0.304 REMARK 500 SER A 29 CA SER A 29 CB -0.339 REMARK 500 LEU A 51 CG LEU A 51 CD1 -0.278 REMARK 500 TYR A 61 CA TYR A 61 CB 0.270 REMARK 500 TYR A 61 CB TYR A 61 CG 0.673 REMARK 500 TYR A 61 CG TYR A 61 CD2 -0.560 REMARK 500 TYR A 61 CG TYR A 61 CD1 0.646 REMARK 500 TYR A 61 CD1 TYR A 61 CE1 -0.393 REMARK 500 LEU A 301 CG LEU A 301 CD1 -0.272 REMARK 500 GLU A 391 C GLU A 391 O -0.384 REMARK 500 ARG A 444 CD ARG A 444 NE -0.263 REMARK 500 PRO A 458 CG PRO A 458 CD -0.378 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 ARG A 24 CB - CG - CD ANGL. DEV. = 20.4 DEGREES REMARK 500 LYS A 26 CG - CD - CE ANGL. DEV. = 19.6 DEGREES REMARK 500 LYS A 26 CD - CE - NZ ANGL. DEV. = 41.9 DEGREES REMARK 500 TYR A 61 CD1 - CE1 - CZ ANGL. DEV. =-19.1 DEGREES REMARK 500 PHE A 100 CA - C - O ANGL. DEV. = 19.0 DEGREES REMARK 500 PHE A 100 O - C - N ANGL. DEV. =-25.1 DEGREES REMARK 500 GLU A 391 CA - C - O ANGL. DEV. =-21.9 DEGREES REMARK 500 GLU A 391 CA - C - N ANGL. DEV. = 17.0 DEGREES REMARK 500 ASN A 393 N - CA - C ANGL. DEV. = 15.5 DEGREES REMARK 500 HIS A 398 N - CA - CB ANGL. DEV. = 31.2 DEGREES REMARK 500 HIS A 398 CA - CB - CG ANGL. DEV. =-21.4 DEGREES REMARK 500 HIS A 398 CA - C - O ANGL. DEV. =-21.1 DEGREES REMARK 500 HIS A 398 C - N - CA ANGL. DEV. = 28.8 DEGREES REMARK 500 HIS A 398 CA - C - N ANGL. DEV. = 20.2 DEGREES REMARK 500 PHE A 404 CA - C - O ANGL. DEV. = 18.2 DEGREES REMARK 500 PHE A 404 O - C - N ANGL. DEV. =-21.7 DEGREES REMARK 500 ARG A 444 CB - CG - CD ANGL. DEV. = 17.3 DEGREES REMARK 500 ARG A 444 CG - CD - NE ANGL. DEV. = 17.1 DEGREES REMARK 500 TYR A 463 CE1 - CZ - OH ANGL. DEV. = 15.3 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 LYS A 117 -115.63 -155.29 REMARK 500 HIS A 332 -48.69 115.68 REMARK 500 ASP A 425 -98.30 52.52 REMARK 500 ALA A 435 -50.50 96.98 REMARK 500 HIS A 438 -39.82 94.02 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 CYS A 454 HIS A 455 58.02 DBREF 1LH9 A 6 476 UNP P18564 ITB6_HUMAN 76 546 SEQRES 1 A 471 GLU ASN PRO VAL SER GLN VAL GLU ILE LEU LYS ASN LYS SEQRES 2 A 471 PRO LEU SER VAL GLY ARG GLN LYS ASN SER SER ASP ILE SEQRES 3 A 471 VAL GLN ILE ALA PRO GLN SER LEU ILE LEU LYS LEU ARG SEQRES 4 A 471 PRO GLY GLY ALA GLN THR LEU GLN VAL HIS VAL ARG GLN SEQRES 5 A 471 THR GLU ASP TYR PRO VAL ASP LEU TYR TYR LEU MET ASP SEQRES 6 A 471 LEU SER ALA SER MET ASP ASP ASP LEU ASN THR ILE LYS SEQRES 7 A 471 GLU LEU GLY SER ARG LEU SER LYS GLU MET SER LYS LEU SEQRES 8 A 471 THR SER ASN PHE ARG LEU GLY PHE GLY SER PHE VAL GLU SEQRES 9 A 471 LYS PRO VAL SER PRO PHE VAL LYS THR THR PRO GLU GLU SEQRES 10 A 471 ILE ALA ASN PRO CYS SER SER ILE PRO TYR PHE CYS LEU SEQRES 11 A 471 PRO THR PHE GLY PHE LYS HIS ILE LEU PRO LEU THR ASN SEQRES 12 A 471 ASP ALA GLU ARG PHE ASN GLU ILE VAL LYS ASN GLN LYS SEQRES 13 A 471 ILE SER ALA ASN ILE ASP THR PRO GLU GLY GLY PHE ASP SEQRES 14 A 471 ALA ILE MET GLN ALA ALA VAL CYS LYS GLU LYS ILE GLY SEQRES 15 A 471 TRP ARG ASN ASP SER LEU HIS LEU LEU VAL PHE VAL SER SEQRES 16 A 471 ASP ALA ASP SER HIS PHE GLY MET ASP SER LYS LEU ALA SEQRES 17 A 471 GLY ILE VAL ILE PRO ASN ASP GLY LEU CYS HIS LEU ASP SEQRES 18 A 471 SER LYS ASN GLU TYR SER MET SER THR VAL LEU GLU TYR SEQRES 19 A 471 PRO THR ILE GLY GLN LEU ILE ASP LYS LEU VAL GLN ASN SEQRES 20 A 471 ASN VAL LEU LEU ILE PHE ALA VAL THR GLN GLU GLN VAL SEQRES 21 A 471 HIS LEU TYR GLU ASN TYR ALA LYS LEU ILE PRO GLY ALA SEQRES 22 A 471 THR VAL GLY LEU LEU GLN LYS ASP SER GLY ASN ILE LEU SEQRES 23 A 471 GLN LEU ILE ILE SER ALA TYR GLU GLU LEU ARG SER GLU SEQRES 24 A 471 VAL GLU LEU GLU VAL LEU GLY ASP THR GLU GLY LEU ASN SEQRES 25 A 471 LEU SER PHE THR ALA ILE CYS ASN ASN GLY THR LEU PHE SEQRES 26 A 471 GLN HIS GLN LYS LYS CYS SER HIS MET LYS VAL GLY ASP SEQRES 27 A 471 THR ALA SER PHE SER VAL THR VAL ASN ILE PRO HIS CYS SEQRES 28 A 471 GLU ARG ARG SER ARG HIS ILE ILE ILE LYS PRO VAL GLY SEQRES 29 A 471 LEU GLY ASP ALA LEU GLU LEU LEU VAL SER PRO GLU CYS SEQRES 30 A 471 ASN CYS ASP CYS GLN LYS GLU VAL GLU VAL ASN SER SER SEQRES 31 A 471 LYS CYS HIS HIS GLY ASN GLY SER PHE GLN CYS GLY VAL SEQRES 32 A 471 CYS ALA CYS HIS PRO GLY HIS MET GLY PRO ARG CYS GLU SEQRES 33 A 471 CYS GLY GLU ASP MET LEU SER THR ASP SER CYS LYS GLU SEQRES 34 A 471 ALA PRO ASP HIS PRO SER CYS SER GLY ARG GLY ASP CYS SEQRES 35 A 471 TYR CYS GLY GLN CYS ILE CYS HIS LEU SER PRO TYR GLY SEQRES 36 A 471 ASN ILE TYR GLY PRO TYR CYS GLN CYS ASP ASN PHE SER SEQRES 37 A 471 CYS VAL ARG HELIX 1 1 SER A 72 ASP A 76 5 5 HELIX 2 2 GLY A 86 LYS A 95 1 10 HELIX 3 3 VAL A 112 VAL A 116 5 5 HELIX 4 4 PRO A 120 ALA A 124 5 5 HELIX 5 5 GLU A 151 ASN A 159 1 9 HELIX 6 6 GLY A 172 CYS A 182 1 11 HELIX 7 7 CYS A 182 GLY A 187 1 6 HELIX 8 8 MET A 208 LEU A 212 5 5 HELIX 9 9 TYR A 231 VAL A 236 5 6 HELIX 10 10 THR A 241 ASN A 252 1 12 HELIX 11 11 GLN A 264 ILE A 275 1 12 HELIX 12 12 SER A 287 ASN A 289 5 3 HELIX 13 13 ILE A 290 ARG A 302 1 13 HELIX 14 14 PRO A 439 ARG A 444 5 6 HELIX 15 15 ASN A 471 VAL A 475 5 5 SHEET 1 A 4 LEU A 39 LEU A 43 0 SHEET 2 A 4 LEU A 374 PRO A 380 1 O SER A 379 N LEU A 43 SHEET 3 A 4 ARG A 361 PRO A 367 -1 N ARG A 361 O VAL A 378 SHEET 4 A 4 LEU A 307 LEU A 310 -1 N GLU A 308 O LYS A 366 SHEET 1 B 2 ALA A 48 LEU A 51 0 SHEET 2 B 2 VAL A 349 ASN A 352 -1 O VAL A 349 N LEU A 51 SHEET 1 C 2 HIS A 54 ARG A 56 0 SHEET 2 C 2 THR A 344 SER A 346 -1 O ALA A 345 N VAL A 55 SHEET 1 D 6 PHE A 140 LYS A 141 0 SHEET 2 D 6 PHE A 100 PHE A 107 -1 N SER A 106 O LYS A 141 SHEET 3 D 6 VAL A 63 ASP A 70 1 N VAL A 63 O ARG A 101 SHEET 4 D 6 LEU A 193 SER A 200 1 O VAL A 197 N LEU A 68 SHEET 5 D 6 LEU A 256 THR A 261 1 O ILE A 257 N LEU A 196 SHEET 6 D 6 THR A 279 LEU A 283 1 O LEU A 283 N VAL A 260 SHEET 1 E 2 ASP A 446 TYR A 448 0 SHEET 2 E 2 GLN A 451 ILE A 453 -1 O GLN A 451 N TYR A 448 SSBOND 1 CYS A 127 CYS A 134 SSBOND 2 CYS A 182 CYS A 223 SSBOND 3 CYS A 324 CYS A 336 SSBOND 4 CYS A 356 CYS A 384 SSBOND 5 CYS A 397 CYS A 406 SSBOND 6 CYS A 411 CYS A 420 SSBOND 7 CYS A 422 CYS A 449 SSBOND 8 CYS A 432 CYS A 447 SSBOND 9 CYS A 441 CYS A 452 CISPEP 1 VAL A 392 ASN A 393 0 4.97 CISPEP 2 LEU A 427 SER A 428 0 24.97 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 MASTER 136 0 0 15 16 0 0 6 0 0 0 37 END