2I63 - Header Asymmetric Unit

HEADER 27-AUG-06 2I63

TITLE THREE-DIMENSIONAL MODEL OF A SIALIC ACID- AND CALCIUM-BOUND TITLE 2 NEURAMINIDASE IN AN AVIAN H5N1 INFLURNZA A VIRUS

COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAMINIDASE IN AN AVIAN H5N1 INFLUENZA A VIRUS; COMPND 3 CHAIN: A

SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFLUENZA A VIRUS; SOURCE 3 STRAIN: H5N1; SOURCE 4 OTHER_DETAILS: A/HANOI/30408/2005(H5N1)

KEYWDS H5N1, INFLUENZA A VIRUSES, SSRNA NEGATIVE-STRAND VIRUSES, KEYWDS 2 ORTHOMYXOVIRIDAE, GENERIC FLU DRUGS, ANTIVIRAL AGENTS, KEYWDS 3 PANDEMIC, AVIAN FLU, AND BIRD FLU

EXPDTA THEORETICAL MODEL

AUTHOR Y.-P.PANG

REVDAT 1 28-AUG-07 2I63 0

JRNL AUTH Y.-P.PANG JRNL TITL THREE-DIMENSIONAL MODELS OF NEURAMINIDASE AND ITS JRNL TITL 2 DRUG-RESISTANT MUTANT IN AVIAN H5N1 INFLUENZA A JRNL TITL 3 VIRUS JRNL REF TO BE PUBLISHED JRNL REFN

REMARK 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 8.0 REMARK 3 AUTHORS : PETER A. KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THIS MODEL WAS PRODUCED FROM REMARK 3 HOMOLOGY MODELING AND REFINEMENT WITH 292 DIFFERENT MOLECULAR REMARK 3 DYNAMICS SIMULATIONS (2.5 NS FOR EACH SIMULATION WITH A 1.0-FS REMARK 3 TIME STEP).

REMARK 4 REMARK 4 2I63 COMPLIES WITH FORMAT V. 3.1, 1-AUG-2007

REMARK 100 REMARK 100 THIS ENTRY WAS DEPOSITED AT RCSB ON 27-AUG-2006.. REMARK 100 THE RCSB ID CODE IS RCSB039183..

REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: THIS MODEL WAS PRODUCED FROM HOMOLOGY MODELING AND REMARK 220 REFINEMENT WITH 292 DIFFERENT MOLECULAR DYNAMICS REMARK 220 SIMULATIONS (2.5 NS FOR EACH SIMULATION WITH A 1.0-FS REMARK 220 TIME STEP). THIS THEORETICAL MODEL ENTRY WAS NOT REMARK 220 ANNOTATED AND NOT VALIDATED BY THE WWPDB STAFF AND REMARK 220 THEREFORE MAY NOT CONFORM TO THE PDB FORMAT.

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; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSEQI REMARK 465 MET A -63 REMARK 465 ASN A -62 REMARK 465 PRO A -61 REMARK 465 ASN A -60 REMARK 465 GLN A -59 REMARK 465 LYS A -58 REMARK 465 ILE A -57 REMARK 465 ILE A -56 REMARK 465 THR A -55 REMARK 465 ILE A -54 REMARK 465 GLY A -53 REMARK 465 SER A -52 REMARK 465 ILE A -51 REMARK 465 CYS A -50 REMARK 465 MET A -49 REMARK 465 VAL A -48 REMARK 465 THR A -47 REMARK 465 GLY A -46 REMARK 465 ILE A -45 REMARK 465 VAL A -44 REMARK 465 SER A -43 REMARK 465 LEU A -42 REMARK 465 MET A -41 REMARK 465 LEU A -40 REMARK 465 GLN A -39 REMARK 465 ILE A -38 REMARK 465 GLY A -37 REMARK 465 ASN A -36 REMARK 465 MET A -35 REMARK 465 ILE A -34 REMARK 465 SER A -33 REMARK 465 ILE A -32 REMARK 465 TRP A -31 REMARK 465 VAL A -30 REMARK 465 SER A -29 REMARK 465 HIS A -28 REMARK 465 SER A -27 REMARK 465 ILE A -26 REMARK 465 HIS A -25 REMARK 465 THR A -24 REMARK 465 GLY A -23 REMARK 465 ASN A -22 REMARK 465 GLN A -21 REMARK 465 HIS A -20 REMARK 465 GLN A -19 REMARK 465 SER A -18 REMARK 465 GLU A -17 REMARK 465 PRO A -16 REMARK 465 ILE A -15 REMARK 465 SER A -14 REMARK 465 ASN A -13 REMARK 465 THR A -12 REMARK 465 LYS A -11 REMARK 465 PHE A -10 REMARK 465 LEU A -9 REMARK 465 THR A -8 REMARK 465 GLU A -7 REMARK 465 LYS A -6 REMARK 465 ALA A -5 REMARK 465 VAL A -4 REMARK 465 ALA A -3 REMARK 465 SER A -2 REMARK 465 VAL A -1 REMARK 465 LYS A 0 REMARK 465 ASP A 384 REMARK 465 LYS A 385

REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BIC A 387

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 386 CA+ REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 210 O REMARK 620 2 GLY A 214 O 88.2 REMARK 620 3 ASP A 240 OD2 75.5 92.2 REMARK 620 4 TYR A 260 O 87.5 174.7 83.7 REMARK 620 N 1 2 3

SEQRES 1 A 449 MET ASN PRO ASN GLN LYS ILE ILE THR ILE GLY SER ILE SEQRES 2 A 449 CYS MET VAL THR GLY ILE VAL SER LEU MET LEU GLN ILE SEQRES 3 A 449 GLY ASN MET ILE SER ILE TRP VAL SER HIS SER ILE HIS SEQRES 4 A 449 THR GLY ASN GLN HIS GLN SER GLU PRO ILE SER ASN THR SEQRES 5 A 449 LYS PHE LEU THR GLU LYS ALA VAL ALA SER VAL LYS LEU SEQRES 6 A 449 ALA GLY ASN SER SER LEU CYS PRO ILE ASN GLY TRP ALA SEQRES 7 A 449 VAL TYR SER LYS ASP ASN SER ILE ARG ILE GLY SER LYS SEQRES 8 A 449 GLY ASP VAL PHE VAL ILE ARG GLU PRO PHE ILE SER CYS SEQRES 9 A 449 SER HIS LEU GLU CYS ARG THR PHE PHE LEU THR GLN GLY SEQRES 10 A 449 ALA LEU LEU ASN ASP LYS HIS SER ASN GLY THR VAL LYS SEQRES 11 A 449 ASP ARG SER PRO HIS ARG THR LEU MET SER CYS PRO VAL SEQRES 12 A 449 GLY GLU ALA PRO SER PRO TYR ASN SER ARG PHE GLU SER SEQRES 13 A 449 VAL ALA TRP SER ALA SER ALA CYS HIS ASP GLY THR SER SEQRES 14 A 449 TRP LEU THR ILE GLY ILE SER GLY PRO ASP ASN GLY ALA SEQRES 15 A 449 VAL ALA VAL VAL LYS TYR ASN GLY ILE ILE THR ASP THR SEQRES 16 A 449 ILE LYS SER TRP ARG ASN ASN ILE LEU ARG THR GLN GLU SEQRES 17 A 449 SER GLU CYS ALA CYS VAL ASN GLY SER CYS PHE THR VAL SEQRES 18 A 449 MET THR ASP GLY PRO SER ASN GLY GLN ALA SER HIS LYS SEQRES 19 A 449 ILE PHE LYS MET GLU LYS GLY LYS VAL VAL LYS SER VAL SEQRES 20 A 449 GLU LEU ASP ALA PRO ASN TYR HIS TYR GLU GLU CYS SER SEQRES 21 A 449 CYS TYR PRO ASP ALA GLY GLU ILE THR CYS VAL CYS ARG SEQRES 22 A 449 ASP ASN TRP HIS GLY SER ASN ARG PRO TRP VAL SER PHE SEQRES 23 A 449 ASN GLN ASN LEU GLU TYR GLN ILE GLY TYR ILE CYS SER SEQRES 24 A 449 GLY VAL PHE GLY ASP ASN PRO ARG PRO ASN ASP GLY THR SEQRES 25 A 449 GLY SER CYS GLY PRO VAL SER SER ASN GLY ALA TYR GLY SEQRES 26 A 449 VAL LYS GLY PHE SER PHE LYS TYR GLY ASN GLY VAL TRP SEQRES 27 A 449 ILE GLY ARG THR LYS SER THR ASN SER ARG SER GLY PHE SEQRES 28 A 449 GLU MET ILE TRP ASP PRO ASN GLY TRP THR GLU THR ASP SEQRES 29 A 449 SER SER PHE SER VAL LYS GLN ASP ILE VAL ALA ILE THR SEQRES 30 A 449 ASP TRP SER GLY TYR SER GLY SER PHE VAL GLN HIS PRO SEQRES 31 A 449 GLU LEU THR GLY LEU ASP CYS ILE ARG PRO CYS PHE TRP SEQRES 32 A 449 VAL GLU LEU ILE ARG GLY ARG PRO LYS GLU SER THR ILE SEQRES 33 A 449 TRP THR SER GLY SER SER ILE SER PHE CYS GLY VAL ASN SEQRES 34 A 449 SER ASP THR VAL GLY TRP SER TRP PRO ASP GLY ALA GLU SEQRES 35 A 449 LEU PRO PHE THR ILE ASP LYS

HET CA+ A 386 1 HET BIC A 387 39 HET HO- A 388 2 HET HO- A 389 2

HETNAM BIC 3-AMINO-3-BENZYL-9-CARBOXAMIDE[4.3.0]BICYCLO-1,6- HETNAM 2 BIC DIAZANONAN-2-ONE

FORMUL 2 CA+ FORMUL 3 BIC C15 H19 N3 O2 FORMUL 4 HO- FORMUL 6 HOH *(H2 O)

HELIX 1 1 ASN A 20 ILE A 24 5 5 HELIX 2 2 GLY A 330 ASP A 332 5 3 HELIX 3 3 GLU A 378 THR A 382 5 5

SHEET 1 A 4 GLY A 12 LYS A 18 0 SHEET 2 A 4 SER A 355 VAL A 364 -1 O SER A 360 N TYR A 16 SHEET 3 A 4 CYS A 333 ARG A 344 -1 N PRO A 336 O GLY A 363 SHEET 4 A 4 SER A 319 THR A 329 -1 N PHE A 322 O CYS A 337 SHEET 1 B 4 PRO A 36 CYS A 40 0 SHEET 2 B 4 CYS A 45 THR A 51 -1 O PHE A 48 N PHE A 37 SHEET 3 B 4 THR A 73 CYS A 77 -1 O THR A 73 N THR A 51 SHEET 4 B 4 ARG A 89 SER A 92 -1 O SER A 92 N LEU A 74 SHEET 1 C 4 SER A 96 CYS A 100 0 SHEET 2 C 4 LEU A 107 SER A 112 -1 O ILE A 109 N SER A 98 SHEET 3 C 4 VAL A 119 TYR A 124 -1 O LYS A 123 N THR A 108 SHEET 4 C 4 ILE A 127 LYS A 133 -1 O THR A 129 N VAL A 122 SHEET 1 D 4 ALA A 148 VAL A 150 0 SHEET 2 D 4 SER A 153 ASP A 160 -1 O SER A 153 N VAL A 150 SHEET 3 D 4 SER A 168 GLU A 175 -1 O MET A 174 N CYS A 154 SHEET 4 D 4 LYS A 178 GLU A 184 -1 O VAL A 180 N LYS A 173 SHEET 1 E 4 GLU A 193 ASP A 200 0 SHEET 2 E 4 GLU A 203 ARG A 209 -1 O VAL A 207 N SER A 196 SHEET 3 E 4 PRO A 218 PHE A 222 -1 O VAL A 220 N CYS A 206 SHEET 4 E 4 TYR A 228 TYR A 232 -1 O GLN A 229 N SER A 221 SHEET 1 F 4 PHE A 265 TYR A 269 0 SHEET 2 F 4 GLY A 272 THR A 278 -1 O TRP A 274 N PHE A 267 SHEET 3 F 4 SER A 285 ASP A 292 -1 O ASP A 292 N VAL A 273 SHEET 4 F 4 VAL A 305 TRP A 315 -1 O GLN A 307 N MET A 289

SSBOND 1 CYS A 8 CYS A 333 1555 1555 2.03 SSBOND 2 CYS A 40 CYS A 45 1555 1555 2.04 SSBOND 3 CYS A 100 CYS A 147 1555 1555 2.04 SSBOND 4 CYS A 149 CYS A 154 1555 1555 2.04 SSBOND 5 CYS A 195 CYS A 208 1555 1555 2.04 SSBOND 6 CYS A 197 CYS A 206 1555 1555 2.04 SSBOND 7 CYS A 234 CYS A 251 1555 1555 2.04 SSBOND 8 CYS A 337 CYS A 362 1555 1555 2.04

LINK O ASP A 210 CA+ CA+ A 386 1555 1555 2.66 LINK O GLY A 214 CA+ CA+ A 386 1555 1555 2.57 LINK OD2 ASP A 240 CA+ CA+ A 386 1555 1555 2.50 LINK O TYR A 260 CA+ CA+ A 386 1555 1555 2.58 LINK CA+ CA+ A 386 O HO- A 388 1555 1555 2.42 LINK CA+ CA+ A 386 O HO- A 389 1555 1555 2.37

CISPEP 1 ASN A 241 PRO A 242 0 -1.86 CISPEP 2 ARG A 346 PRO A 347 0 1.99

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