10 20 30 40 50 60 70 80 2PTE - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE(TRANSPEPTIDASE) 16-NOV-90 2PTE
TITLE DIFFERENT MODES OF VANCOMYCIN AND D-ALANYL-D-ALANINE TITLE 2 PEPTIDASE BINDING TO CELL WALL PEPTIDE AND A POSSIBLE ROLE TITLE 3 FOR THE VANCOMYCIN RESISTANCE PROTEIN
COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANYL-D-ALANINE CARBOXYPEPTIDASE; COMPND 3 CHAIN: E; COMPND 4 EC: 3.4.16.4; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE:; COMPND 8 CHAIN: P; COMPND 9 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 MOL_ID: 2
KEYWDS HYDROLASE(TRANSPEPTIDASE)
EXPDTA THEORETICAL MODEL
AUTHOR J.R.KNOX
REVDAT 1 31-JAN-94 2PTE 0
JRNL AUTH J.R.KNOX,R.F.PRATT JRNL TITL DIFFERENT MODES OF VANCOMYCIN AND JRNL TITL 2 D-ALANYL-D-ALANINE PEPTIDASE BINDING TO CELL WALL JRNL TITL 3 PEPTIDE AND A POSSIBLE ROLE FOR THE VANCOMYCIN JRNL TITL 4 RESISTANCE PROTEIN. JRNL REF ANTIMICROB.AGENTS CHEMOTHER. V. 34 1342 1990 JRNL REFN ASTM AMACCQ US ISSN 7066-4804
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.A.KELLY,J.R.KNOX,H.ZHAO,J.-M.FRERE,J.-M.GHUYSEN REMARK 1 TITL CRYSTALLOGRAPHIC MAPPING OF BETA-LACTAMS BOUND TO REMARK 1 TITL 2 A D-ALANYL-D-ALANINE PEPTIDASE TARGET ENZYME REMARK 1 REF J.MOL.BIOL. V. 209 281 1989 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836
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 2PTE COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998
REMARK 5 REMARK 5 THIS ENTRY REPRESENTS THE MODELLED BINDING OF THE KAA REMARK 5 TRIPEPTIDE L-LYS-D-ALA-D-ALA TO ACTIVE SITE PEPTIDES REMARK 5 D-ALA-D-ALANINE-TRANSPEPTIDASE/CARBOXYPEPTIDASE (PROTEIN REMARK 5 DATA BANK ENTRY 1PTE). SEE FIGURE 2B IN REFERENCE 1 REMARK 5 ABOVE.
REMARK 6 REMARK 6 CHAIN *P* DENOTES THE KAA TRIPEPTIDE. SIX PEPTIDE REMARK 6 FRAGMENTS FROM THE ENZYME CHAIN *E* ARE GIVEN: 61 - 65, REMARK 6 94 - 95, 159 - 164, 224 - 228, 279 -283, AND 298 - 302.
REMARK 7 REMARK 7 SEQUENCE ADVISORY NOTICE: REMARK 7 DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. REMARK 7 REMARK 7 SWISS-PROT ENTRY NAME:DAC_STRSQ REMARK 7 REMARK 7 SWISS-PROT RESIDUE PDB SEQRES REMARK 7 NAME NUMBER NAME CHAIN SEQ/INSERT CODE REMARK 7 ASN 306 ASP E 225 REMARK 7 GLN 309 GLU E 228
REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL
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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ALA E 1 REMARK 465 ASP E 2 REMARK 465 LEU E 3 REMARK 465 PRO E 4 REMARK 465 ALA E 5 REMARK 465 PRO E 6 REMARK 465 ASP E 7 REMARK 465 ASP E 8 REMARK 465 THR E 9 REMARK 465 GLY E 10 REMARK 465 LEU E 11 REMARK 465 GLN E 12 REMARK 465 ALA E 13 REMARK 465 VAL E 14 REMARK 465 LEU E 15 REMARK 465 HIS E 16 REMARK 465 THR E 17 REMARK 465 ALA E 18 REMARK 465 LEU E 19 REMARK 465 SER E 20 REMARK 465 GLN E 21 REMARK 465 GLY E 22 REMARK 465 ALA E 23 REMARK 465 PRO E 24 REMARK 465 GLY E 25 REMARK 465 ALA E 26 REMARK 465 MET E 27 REMARK 465 VAL E 28 REMARK 465 ARG E 29 REMARK 465 VAL E 30 REMARK 465 ASP E 31 REMARK 465 ASP E 32 REMARK 465 ASN E 33 REMARK 465 GLY E 34 REMARK 465 THR E 35 REMARK 465 ILE E 36 REMARK 465 HIS E 37 REMARK 465 GLN E 38 REMARK 465 LEU E 39 REMARK 465 SER E 40 REMARK 465 GLU E 41 REMARK 465 GLY E 42 REMARK 465 VAL E 43 REMARK 465 ALA E 44 REMARK 465 ASP E 45 REMARK 465 ARG E 46 REMARK 465 ALA E 47 REMARK 465 THR E 48 REMARK 465 GLY E 49 REMARK 465 ARG E 50 REMARK 465 ALA E 51 REMARK 465 ILE E 52 REMARK 465 THR E 53 REMARK 465 THR E 54 REMARK 465 THR E 55 REMARK 465 ASP E 56 REMARK 465 ARG E 57 REMARK 465 PHE E 58 REMARK 465 ARG E 59 REMARK 465 VAL E 60 REMARK 465 SER E 66 REMARK 465 PHE E 67 REMARK 465 SER E 68 REMARK 465 ALA E 69 REMARK 465 VAL E 70 REMARK 465 VAL E 71 REMARK 465 LEU E 72 REMARK 465 LEU E 73 REMARK 465 GLN E 74 REMARK 465 LEU E 75 REMARK 465 VAL E 76 REMARK 465 ASP E 77 REMARK 465 GLU E 78 REMARK 465 GLY E 79 REMARK 465 LYS E 80 REMARK 465 LEU E 81 REMARK 465 ASP E 82 REMARK 465 LEU E 83 REMARK 465 ASP E 84 REMARK 465 ALA E 85 REMARK 465 SER E 86 REMARK 465 VAL E 87 REMARK 465 ASN E 88 REMARK 465 THR E 89 REMARK 465 TYR E 90 REMARK 465 LEU E 91 REMARK 465 PRO E 92 REMARK 465 GLY E 93 REMARK 465 PRO E 96 REMARK 465 ASP E 97 REMARK 465 ASP E 98 REMARK 465 ARG E 99 REMARK 465 ILE E 100 REMARK 465 THR E 101 REMARK 465 VAL E 102 REMARK 465 ARG E 103 REMARK 465 GLN E 104 REMARK 465 VAL E 105 REMARK 465 MET E 106 REMARK 465 SER E 107 REMARK 465 HIS E 108 REMARK 465 ARG E 109 REMARK 465 SER E 110 REMARK 465 GLY E 111 REMARK 465 LEU E 112 REMARK 465 TYR E 113 REMARK 465 ASP E 114 REMARK 465 TYR E 115 REMARK 465 THR E 116 REMARK 465 ASN E 117 REMARK 465 ASP E 118 REMARK 465 MET E 119 REMARK 465 PHE E 120 REMARK 465 ALA E 121 REMARK 465 GLN E 122 REMARK 465 THR E 123 REMARK 465 VAL E 124 REMARK 465 PRO E 125 REMARK 465 GLY E 126 REMARK 465 PHE E 127 REMARK 465 GLU E 128 REMARK 465 SER E 129 REMARK 465 VAL E 130 REMARK 465 ARG E 131 REMARK 465 ASN E 132 REMARK 465 LYS E 133 REMARK 465 VAL E 134 REMARK 465 PHE E 135 REMARK 465 SER E 136 REMARK 465 TYR E 137 REMARK 465 GLN E 138 REMARK 465 ASP E 139 REMARK 465 LEU E 140 REMARK 465 ILE E 141 REMARK 465 THR E 142 REMARK 465 LEU E 143 REMARK 465 SER E 144 REMARK 465 LEU E 145 REMARK 465 LYS E 146 REMARK 465 HIS E 147 REMARK 465 GLY E 148 REMARK 465 VAL E 149 REMARK 465 THR E 150 REMARK 465 ASN E 151 REMARK 465 ALA E 152 REMARK 465 PRO E 153 REMARK 465 GLY E 154 REMARK 465 ALA E 155 REMARK 465 ALA E 156 REMARK 465 TYR E 157 REMARK 465 SER E 158 REMARK 465 VAL E 164A REMARK 465 VAL E 164B REMARK 465 ALA E 164C REMARK 465 GLY E 164D REMARK 465 MET E 164E REMARK 465 LEU E 164F REMARK 465 ILE E 164G REMARK 465 GLU E 164H REMARK 465 LYS E 164I REMARK 465 LEU E 164J REMARK 465 THR E 164K REMARK 465 GLY E 164L REMARK 465 HIS E 164M REMARK 465 SER E 164N REMARK 465 VAL E 164O REMARK 465 ALA E 164P REMARK 465 THR E 164Q REMARK 465 GLU E 164R REMARK 465 TYR E 164S REMARK 465 GLN E 164T REMARK 465 ASN E 164U REMARK 465 ARG E 164V REMARK 465 ILE E 164W REMARK 465 PHE E 164X REMARK 465 THR E 164Y REMARK 465 PRO E 164Z REMARK 465 LEU E 165A REMARK 465 ASN E 165B REMARK 465 LEU E 165C REMARK 465 THR E 165D REMARK 465 ASP E 165E REMARK 465 THR E 165F REMARK 465 PHE E 165G REMARK 465 TYR E 165H REMARK 465 VAL E 165I REMARK 465 HIS E 165J REMARK 465 PRO E 165K REMARK 465 ASP E 165L REMARK 465 THR E 165M REMARK 465 VAL E 165N REMARK 465 ILE E 165O REMARK 465 PRO E 165P REMARK 465 GLY E 165Q REMARK 465 THR E 165R REMARK 465 HIS E 165S REMARK 465 ALA E 165T REMARK 465 ASN E 165U REMARK 465 GLY E 165V REMARK 465 TYR E 165W REMARK 465 LEU E 165X REMARK 465 THR E 165Y REMARK 465 PRO E 165Z REMARK 465 ASP E 166A REMARK 465 GLU E 166B REMARK 465 ALA E 166C REMARK 465 GLY E 166D REMARK 465 GLY E 166E REMARK 465 ALA E 166F REMARK 465 LEU E 166G REMARK 465 VAL E 166H REMARK 465 ASP E 166I REMARK 465 SER E 166J REMARK 465 THR E 166K REMARK 465 GLU E 166L REMARK 465 GLN E 166M REMARK 465 THR E 166N REMARK 465 VAL E 166O REMARK 465 SER E 166P REMARK 465 TRP E 166Q REMARK 465 ALA E 166R REMARK 465 GLN E 166S REMARK 465 THR E 166T REMARK 465 GLY E 166U REMARK 465 ALA E 166V REMARK 465 ALA E 166W REMARK 465 VAL E 166X REMARK 465 ILE E 166Y REMARK 465 SER E 166Z REMARK 465 SER E 167A REMARK 465 THR E 167B REMARK 465 GLN E 167C REMARK 465 ASP E 167D REMARK 465 LEU E 167E REMARK 465 ASP E 167F REMARK 465 THR E 167G REMARK 465 PHE E 167H REMARK 465 PHE E 167I REMARK 465 SER E 167J REMARK 465 ALA E 167K REMARK 465 LEU E 167L REMARK 465 MET E 167M REMARK 465 SER E 167N REMARK 465 GLY E 167O REMARK 465 GLN E 167P REMARK 465 LEU E 167Q REMARK 465 MET E 167R REMARK 465 SER E 167S REMARK 465 ALA E 167T REMARK 465 ALA E 167U REMARK 465 GLN E 167V REMARK 465 LEU E 167W REMARK 465 ALA E 167X REMARK 465 GLN E 167Y REMARK 465 MET E 167Z REMARK 465 GLN E 168A REMARK 465 GLN E 168B REMARK 465 TRP E 168C REMARK 465 THR E 168D REMARK 465 THR E 168E REMARK 465 LEU E 284 REMARK 465 ARG E 285 REMARK 465 ARG E 286 REMARK 465 ARG E 287 REMARK 465 ASP E 288 REMARK 465 LEU E 289 REMARK 465 SER E 290 REMARK 465 CYS E 291 REMARK 465 GLY E 292 REMARK 465 ILE E 293 REMARK 465 SER E 294 REMARK 465 VAL E 295 REMARK 465 TYR E 296 REMARK 465 GLY E 297 REMARK 465 GLN E 303 REMARK 465 GLY E 304 REMARK 465 TYR E 305 REMARK 465 TYR E 306 REMARK 465 THR E 307 REMARK 465 TYR E 308 REMARK 465 ALA E 309 REMARK 465 PHE E 310 REMARK 465 ALA E 311 REMARK 465 SER E 312 REMARK 465 LYS E 313 REMARK 465 ASP E 314 REMARK 465 GLY E 315 REMARK 465 GLN E 316 REMARK 465 ALA E 317 REMARK 465 HIS E 318 REMARK 465 VAL E 319 REMARK 465 THR E 320 REMARK 465 ALA E 321 REMARK 465 LEU E 322 REMARK 465 ALA E 323 REMARK 465 ASN E 324 REMARK 465 THR E 325 REMARK 465 SER E 326 REMARK 465 ASN E 327 REMARK 465 ASN E 328 REMARK 465 VAL E 329 REMARK 465 ASN E 330 REMARK 465 VAL E 331 REMARK 465 LEU E 332 REMARK 465 ASN E 333 REMARK 465 THR E 334 REMARK 465 MET E 335 REMARK 465 ALA E 336 REMARK 465 ARG E 337 REMARK 465 THR E 338 REMARK 465 LEU E 339 REMARK 465 GLU E 340 REMARK 465 SER E 341 REMARK 465 ALA E 342 REMARK 465 PHE E 343 REMARK 465 CYS E 344 REMARK 465 GLY E 345 REMARK 465 LYS E 346 REMARK 465 PRO E 347 REMARK 465 THR E 348 REMARK 465 THR E 349
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 OG SER E 62 OXT ALA P 3 1.41 REMARK 500 OG SER E 62 N ALA P 3 1.63 REMARK 500 CZ PHE E 164 CB ALA P 2 1.66 REMARK 500 OG SER E 62 C ALA P 3 1.78 REMARK 500 OG SER E 62 C ALA P 2 1.94 REMARK 500 CB SER E 62 OXT ALA P 3 1.96 REMARK 500 OG SER E 62 CA ALA P 3 2.04 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 SER E 160 111.76 114.57 REMARK 500 ALA P 2 -120.29 145.08 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 THR E 301 VAL E 302 143.81
DBREF 2PTE E 1 349 UNP P15555 DAC_STRSQ 32 380
SEQADV 2PTE THR E 186 UNP P15555 SER 267 CONFLICT SEQADV 2PTE GLY E 187 UNP P15555 ALA 268 CONFLICT SEQADV 2PTE ALA E 188 UNP P15555 GLY 269 CONFLICT SEQADV 2PTE ASP E 225 UNP P15555 ASN 306 CONFLICT SEQADV 2PTE GLU E 228 UNP P15555 GLN 309 CONFLICT SEQADV 2PTE GLN E 316 UNP P15555 LYS 347 CONFLICT SEQADV 2PTE ALA E 317 UNP P15555 ARG 348 CONFLICT SEQADV 2PTE HIS E 318 UNP P15555 SER 349 CONFLICT
SEQRES 1 E 349 ALA ASP LEU PRO ALA PRO ASP ASP THR GLY LEU GLN ALA SEQRES 2 E 349 VAL LEU HIS THR ALA LEU SER GLN GLY ALA PRO GLY ALA SEQRES 3 E 349 MET VAL ARG VAL ASP ASP ASN GLY THR ILE HIS GLN LEU SEQRES 4 E 349 SER GLU GLY VAL ALA ASP ARG ALA THR GLY ARG ALA ILE SEQRES 5 E 349 THR THR THR ASP ARG PHE ARG VAL GLY SER VAL THR LYS SEQRES 6 E 349 SER PHE SER ALA VAL VAL LEU LEU GLN LEU VAL ASP GLU SEQRES 7 E 349 GLY LYS LEU ASP LEU ASP ALA SER VAL ASN THR TYR LEU SEQRES 8 E 349 PRO GLY LEU LEU PRO ASP ASP ARG ILE THR VAL ARG GLN SEQRES 9 E 349 VAL MET SER HIS ARG SER GLY LEU TYR ASP TYR THR ASN SEQRES 10 E 349 ASP MET PHE ALA GLN THR VAL PRO GLY PHE GLU SER VAL SEQRES 11 E 349 ARG ASN LYS VAL PHE SER TYR GLN ASP LEU ILE THR LEU SEQRES 12 E 349 SER LEU LYS HIS GLY VAL THR ASN ALA PRO GLY ALA ALA SEQRES 13 E 349 TYR SER TYR SER ASN THR ASN PHE VAL VAL ALA GLY MET SEQRES 14 E 349 LEU ILE GLU LYS LEU THR GLY HIS SER VAL ALA THR GLU SEQRES 15 E 349 TYR GLN ASN ARG ILE PHE THR PRO LEU ASN LEU THR ASP SEQRES 16 E 349 THR PHE TYR VAL HIS PRO ASP THR VAL ILE PRO GLY THR SEQRES 17 E 349 HIS ALA ASN GLY TYR LEU THR PRO ASP GLU ALA GLY GLY SEQRES 18 E 349 ALA LEU VAL ASP SER THR GLU GLN THR VAL SER TRP ALA SEQRES 19 E 349 GLN THR GLY ALA ALA VAL ILE SER SER THR GLN ASP LEU SEQRES 20 E 349 ASP THR PHE PHE SER ALA LEU MET SER GLY GLN LEU MET SEQRES 21 E 349 SER ALA ALA GLN LEU ALA GLN MET GLN GLN TRP THR THR SEQRES 22 E 349 VAL ASP SER THR GLU GLY TYR GLY LEU GLY LEU ARG ARG SEQRES 23 E 349 ARG ASP LEU SER CYS GLY ILE SER VAL TYR GLY HIS THR SEQRES 24 E 349 GLY THR VAL GLN GLY TYR TYR THR TYR ALA PHE ALA SER SEQRES 25 E 349 LYS ASP GLY GLN ALA HIS VAL THR ALA LEU ALA ASN THR SEQRES 26 E 349 SER ASN ASN VAL ASN VAL LEU ASN THR MET ALA ARG THR SEQRES 27 E 349 LEU GLU SER ALA PHE CYS GLY LYS PRO THR THR SEQRES 1 P 3 LYS ALA ALA
FTNOTE 1 THR E 301 - VAL E 302 OMEGA =143.81 PEPTIDE BOND DEVIATES FTNOTE 1 SIGNIFICANTLY FROM TRANS CONFORMATION FTNOTE 2 RESIDUES ALA P 2 AND ALA P 3 ARE D AMINO ACIDS.
HELIX 1 1 GLY E 61 LYS E 65 5 5
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