0.011173 0.000000 0.000000 0.000000 0.011173 0.000000 0.000000 0.000000 0.007547 0.00000 0.00000 0.00000 Scott, D.L. Otwinowski, Z. Sigler, P.B. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 16 90.00 90.00 90.00 89.500 89.500 132.500 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking Ca 2 40.078 CALCIUM ION non-polymer C3 H7 N O2 S 121.158 y CYSTEINE L-peptide linking C20 H45 N O8 P2 489.521 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE non-polymer C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 S 149.211 y METHIONINE L-peptide linking C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Science SCIEAS 0038 0036-8075 250 1563 1566 2274788 Crystal structure of bee-venom phospholipase A2 in a complex with a transition-state analogue. 1990 US Science SCIEAS 0038 0036-8075 250 1541 Interfacial Catalysis: The Mechanism of Phospholipase A2 1990 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 1 x-ray 1 1.0 15274.324 PHOSPHOLIPASE A2 3.1.1.4 1 man polymer 40.078 CALCIUM ION 1 syn non-polymer 489.521 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE 1 syn non-polymer 18.015 water 80 nat water no no IIYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTNTASHTRLSCDCDDKFYDCLKNSADTISS YFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY IIYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTNTASHTRLSCDCDDKFYDCLKNSADTISS YFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLRKY A polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n honey bee Apis sample 7460 Apis mellifera 4.34 71.67 pdbx_database_status software software repository Initial release Version format compliance Version format compliance Data collection Other Refinement description Data collection Refinement description 1 0 1993-10-31 1 1 2008-03-03 1 2 2011-07-13 1 3 2019-07-17 1 4 2019-08-14 _pdbx_database_status.process_site _software.classification _software.classification Y BNL 1992-09-07 REL CA CALCIUM ION GEL 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE HOH water CA 501 2 CA CA 501 A GEL 420 3 GEL GEL 420 A HOH 201 4 HOH HOH 201 A HOH 202 4 HOH HOH 202 A HOH 203 4 HOH HOH 203 A HOH 204 4 HOH HOH 204 A HOH 205 4 HOH HOH 205 A HOH 206 4 HOH HOH 206 A HOH 207 4 HOH HOH 207 A HOH 208 4 HOH HOH 208 A HOH 209 4 HOH HOH 209 A HOH 210 4 HOH HOH 210 A HOH 211 4 HOH HOH 211 A HOH 212 4 HOH HOH 212 A HOH 213 4 HOH HOH 213 A HOH 214 4 HOH HOH 214 A HOH 215 4 HOH HOH 215 A HOH 216 4 HOH HOH 216 A HOH 217 4 HOH HOH 217 A HOH 218 4 HOH HOH 218 A HOH 219 4 HOH HOH 219 A HOH 220 4 HOH HOH 220 A HOH 221 4 HOH HOH 221 A HOH 222 4 HOH HOH 222 A HOH 223 4 HOH HOH 223 A HOH 224 4 HOH HOH 224 A HOH 225 4 HOH HOH 225 A HOH 226 4 HOH HOH 226 A HOH 227 4 HOH HOH 227 A HOH 228 4 HOH HOH 228 A HOH 229 4 HOH HOH 229 A HOH 230 4 HOH HOH 230 A HOH 231 4 HOH HOH 231 A HOH 232 4 HOH HOH 232 A HOH 233 4 HOH HOH 233 A HOH 234 4 HOH HOH 234 A HOH 235 4 HOH HOH 235 A HOH 236 4 HOH HOH 236 A HOH 237 4 HOH HOH 237 A HOH 238 4 HOH HOH 238 A HOH 239 4 HOH HOH 239 A HOH 240 4 HOH HOH 240 A HOH 241 4 HOH HOH 241 A HOH 242 4 HOH HOH 242 A HOH 243 4 HOH HOH 243 A HOH 244 4 HOH HOH 244 A HOH 245 4 HOH HOH 245 A HOH 246 4 HOH HOH 246 A HOH 247 4 HOH HOH 247 A HOH 248 4 HOH HOH 248 A HOH 249 4 HOH HOH 249 A HOH 250 4 HOH HOH 250 A HOH 251 4 HOH HOH 251 A HOH 252 4 HOH HOH 252 A HOH 253 4 HOH HOH 253 A HOH 254 4 HOH HOH 254 A HOH 255 4 HOH HOH 255 A HOH 256 4 HOH HOH 256 A HOH 257 4 HOH HOH 257 A HOH 258 4 HOH HOH 258 A HOH 259 4 HOH HOH 259 A HOH 260 4 HOH HOH 260 A HOH 261 4 HOH HOH 261 A HOH 262 4 HOH HOH 262 A HOH 263 4 HOH HOH 263 A HOH 264 4 HOH HOH 264 A HOH 265 4 HOH HOH 265 A HOH 266 4 HOH HOH 266 A HOH 267 4 HOH HOH 267 A HOH 268 4 HOH HOH 268 A HOH 269 4 HOH HOH 269 A HOH 270 4 HOH HOH 270 A HOH 271 4 HOH HOH 271 A HOH 272 4 HOH HOH 272 A HOH 273 4 HOH HOH 273 A HOH 274 4 HOH HOH 274 A HOH 275 4 HOH HOH 275 A HOH 276 4 HOH HOH 276 A HOH 277 4 HOH HOH 277 A HOH 278 4 HOH HOH 278 A HOH 279 4 HOH HOH 279 A HOH 280 4 HOH HOH 280 A ILE 1 n 1 ILE 1 A ILE 2 n 2 ILE 2 A TYR 3 n 3 TYR 3 A PRO 4 n 4 PRO 4 A GLY 5 n 5 GLY 5 A THR 6 n 6 THR 6 A LEU 7 n 7 LEU 7 A TRP 8 n 8 TRP 8 A CYS 9 n 9 CYS 9 A GLY 10 n 10 GLY 10 A HIS 11 n 11 HIS 11 A GLY 12 n 12 GLY 12 A ASN 13 n 13 ASN 13 A LYS 14 n 14 LYS 14 A SER 15 n 15 SER 15 A SER 16 n 16 SER 16 A GLY 17 n 17 GLY 17 A PRO 18 n 18 PRO 18 A ASN 19 n 19 ASN 19 A GLU 20 n 20 GLU 20 A LEU 21 n 21 LEU 21 A GLY 22 n 22 GLY 22 A ARG 23 n 23 ARG 23 A PHE 24 n 24 PHE 24 A LYS 25 n 25 LYS 25 A HIS 26 n 26 HIS 26 A THR 27 n 27 THR 27 A ASP 28 n 28 ASP 28 A ALA 29 n 29 ALA 29 A CYS 30 n 30 CYS 30 A CYS 31 n 31 CYS 31 A ARG 32 n 32 ARG 32 A THR 33 n 33 THR 33 A HIS 34 n 34 HIS 34 A ASP 35 n 35 ASP 35 A MET 36 n 36 MET 36 A CYS 37 n 37 CYS 37 A PRO 38 n 38 PRO 38 A ASP 39 n 39 ASP 39 A VAL 40 n 40 VAL 40 A MET 41 n 41 MET 41 A SER 42 n 42 SER 42 A ALA 43 n 43 ALA 43 A GLY 44 n 44 GLY 44 A GLU 45 n 45 GLU 45 A SER 46 n 46 SER 46 A LYS 47 n 47 LYS 47 A HIS 48 n 48 HIS 48 A GLY 49 n 49 GLY 49 A LEU 50 n 50 LEU 50 A THR 51 n 51 THR 51 A ASN 52 n 52 ASN 52 A THR 53 n 53 THR 53 A ALA 54 n 54 ALA 54 A SER 55 n 55 SER 55 A HIS 56 n 56 HIS 56 A THR 57 n 57 THR 57 A ARG 58 n 58 ARG 58 A LEU 59 n 59 LEU 59 A SER 60 n 60 SER 60 A CYS 61 n 61 CYS 61 A ASP 62 n 62 ASP 62 A CYS 63 n 63 CYS 63 A ASP 64 n 64 ASP 64 A ASP 65 n 65 ASP 65 A LYS 66 n 66 LYS 66 A PHE 67 n 67 PHE 67 A TYR 68 n 68 TYR 68 A ASP 69 n 69 ASP 69 A CYS 70 n 70 CYS 70 A LEU 71 n 71 LEU 71 A LYS 72 n 72 LYS 72 A ASN 73 n 73 ASN 73 A SER 74 n 74 SER 74 A ALA 75 n 75 ALA 75 A ASP 76 n 76 ASP 76 A THR 77 n 77 THR 77 A ILE 78 n 78 ILE 78 A SER 79 n 79 SER 79 A SER 80 n 80 SER 80 A TYR 81 n 81 TYR 81 A PHE 82 n 82 PHE 82 A VAL 83 n 83 VAL 83 A GLY 84 n 84 GLY 84 A LYS 85 n 85 LYS 85 A MET 86 n 86 MET 86 A TYR 87 n 87 TYR 87 A PHE 88 n 88 PHE 88 A ASN 89 n 89 ASN 89 A LEU 90 n 90 LEU 90 A ILE 91 n 91 ILE 91 A ASP 92 n 92 ASP 92 A THR 93 n 93 THR 93 A LYS 94 n 94 LYS 94 A CYS 95 n 95 CYS 95 A TYR 96 n 96 TYR 96 A LYS 97 n 97 LYS 97 A LEU 98 n 98 LEU 98 A GLU 99 n 99 GLU 99 A HIS 100 n 100 HIS 100 A PRO 101 n 101 PRO 101 A VAL 102 n 102 VAL 102 A THR 103 n 103 THR 103 A GLY 104 n 104 GLY 104 A CYS 105 n 105 CYS 105 A GLY 106 n 106 GLY 106 A GLU 107 n 107 GLU 107 A ARG 108 n 108 ARG 108 A THR 109 n 109 THR 109 A GLU 110 n 110 GLU 110 A GLY 111 n 111 GLY 111 A ARG 112 n 112 ARG 112 A CYS 113 n 113 CYS 113 A LEU 114 n 114 LEU 114 A HIS 115 n 115 HIS 115 A TYR 116 n 116 TYR 116 A THR 117 n 117 THR 117 A VAL 118 n 118 VAL 118 A ASP 119 n 119 ASP 119 A LYS 120 n 120 LYS 120 A SER 121 n 121 SER 121 A LYS 122 n 122 LYS 122 A PRO 123 n 123 PRO 123 A LYS 124 n 124 LYS 124 A VAL 125 n 125 VAL 125 A TYR 126 n 126 TYR 126 A GLN 127 n 127 GLN 127 A TRP 128 n 128 TRP 128 A PHE 129 n 129 PHE 129 A ASP 130 n 130 ASP 130 A LEU 131 n 131 LEU 131 A ARG 132 n 132 ARG 132 A LYS 133 n 133 LYS 133 A TYR 134 n 134 TYR 134 A author_defined_assembly 2 dimeric A TRP 8 A O TRP 8 1_555 A CA 501 B CA CA 1_555 A GLY 12 A O GLY 12 1_555 88.5 A TRP 8 A O TRP 8 1_555 A CA 501 B CA CA 1_555 A ASP 35 A OD2 ASP 35 1_555 94.8 A GLY 12 A O GLY 12 1_555 A CA 501 B CA CA 1_555 A ASP 35 A OD2 ASP 35 1_555 74.1 A TRP 8 A O TRP 8 1_555 A CA 501 B CA CA 1_555 A GLY 10 A O GLY 10 1_555 97.2 A GLY 12 A O GLY 12 1_555 A CA 501 B CA CA 1_555 A GLY 10 A O GLY 10 1_555 79.5 A ASP 35 A OD2 ASP 35 1_555 A CA 501 B CA CA 1_555 A GLY 10 A O GLY 10 1_555 150.7 A TRP 8 A O TRP 8 1_555 A CA 501 B CA CA 1_555 A ASP 35 A OD1 ASP 35 1_555 100.8 A GLY 12 A O GLY 12 1_555 A CA 501 B CA CA 1_555 A ASP 35 A OD1 ASP 35 1_555 128.8 A ASP 35 A OD2 ASP 35 1_555 A CA 501 B CA CA 1_555 A ASP 35 A OD1 ASP 35 1_555 55.1 A GLY 10 A O GLY 10 1_555 A CA 501 B CA CA 1_555 A ASP 35 A OD1 ASP 35 1_555 146.4 A TRP 8 A O TRP 8 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O4P GEL 1_555 179.3 A GLY 12 A O GLY 12 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O4P GEL 1_555 91.8 A ASP 35 A OD2 ASP 35 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O4P GEL 1_555 85.9 A GLY 10 A O GLY 10 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O4P GEL 1_555 82.3 A ASP 35 A OD1 ASP 35 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O4P GEL 1_555 79.5 A TRP 8 A O TRP 8 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 76.4 A GLY 12 A O GLY 12 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 149.5 A ASP 35 A OD2 ASP 35 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 132.7 A GLY 10 A O GLY 10 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 76.3 A ASP 35 A OD1 ASP 35 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 80.6 A GEL 420 C O4P GEL 1_555 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 103.0 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 10_665 -x+1,-y+1,z crystal symmetry operation 89.5000000000 89.5000000000 0.0000000000 A N MET 41 A N MET 41 A O ARG 58 A O ARG 58 A O LYS 47 A O LYS 47 A N LEU 50 A N LEU 50 A O GLU 99 A O GLU 99 A N VAL 125 A N VAL 125 A N THR 103 A N THR 103 A O THR 117 A O THR 117 1 A A O NH2 PHE ARG 88 112 1.89 1 A A OE1 OE2 GLU GLU 107 110 2.19 1 3.40 0.50 120.30 123.70 A A A NE CZ NH2 ARG ARG ARG 32 32 32 N 1 10.08 1.60 100.20 110.28 A A A CG SD CE MET MET MET 41 41 41 N 1 3.45 0.50 120.30 123.75 A A A NE CZ NH2 ARG ARG ARG 58 58 58 N 1 26.63 2.30 111.70 138.33 A A A CD CE NZ LYS LYS LYS 85 85 85 N 1 3.32 0.50 120.30 123.62 A A A NE CZ NH2 ARG ARG ARG 108 108 108 N 1 26.37 2.60 111.60 137.97 A A A CB CG CD LYS LYS LYS 122 122 122 N 1 34.76 3.00 111.90 146.66 A A A CG CD CE LYS LYS LYS 122 122 122 N 1 6.73 0.90 118.30 125.03 A A A CB CG OD1 ASP ASP ASP 130 130 130 N 1 -5.89 0.90 118.30 112.41 A A A CB CG OD2 ASP ASP ASP 130 130 130 N 1 36.94 1.40 123.60 160.54 A A A CD NE CZ ARG ARG ARG 132 132 132 N 1 6.49 0.50 120.30 126.79 A A A NE CZ NH1 ARG ARG ARG 132 132 132 N 1 -3.19 0.50 120.30 117.11 A A A NE CZ NH2 ARG ARG ARG 132 132 132 N 1 A A O O HOH HOH 241 244 1.06 1_555 6_555 1 A A O O HOH HOH 244 247 2.02 1_555 6_555 1 A A NH1 O ARG HOH 23 224 2.15 1_555 10_665 1 A GLU 107 -6.04 76.32 1 A ARG 108 -60.59 7.32 1 A THR 109 165.05 91.22 1 A GLU 110 -23.88 164.91 1 A HIS 115 -117.85 74.79 0.192 0.192 2.0 1 2.0 80 1177 32 0 1065 0.017 2.10 model building X-PLOR refinement PROFFT refinement X-PLOR phasing X-PLOR PHOSPHOLIPASE A2 (E.C.3.1.1.4) COMPLEX WITH THE TRANSITION-STATE ANALOGUE CRYSTAL STRUCTURE OF BEE-VENOM PHOSPHOLIPASE A2 IN A COMPLEX WITH A TRANSITION-STATE ANALOGUE 1 N N 2 N N 3 N N 4 N N A PHE 24 A PHE 24 HELX_P A CYS 37 A CYS 37 1 H1 14 A CYS 61 A CYS 61 HELX_P A SER 74 A SER 74 1 H2 14 A ASP 76 A ASP 76 HELX_P A ASN 89 A ASN 89 1 H3 14 disulf 2.012 A CYS 9 A SG CYS 9 1_555 A CYS 31 A SG CYS 31 1_555 disulf 1.767 A CYS 30 A SG CYS 30 1_555 A CYS 70 A SG CYS 70 1_555 disulf 1.979 A CYS 37 A SG CYS 37 1_555 A CYS 63 A SG CYS 63 1_555 disulf 2.034 A CYS 61 A SG CYS 61 1_555 A CYS 95 A SG CYS 95 1_555 disulf 1.928 A CYS 105 A SG CYS 105 1_555 A CYS 113 A SG CYS 113 1_555 metalc 2.351 A CA 501 B CA CA 1_555 A TRP 8 A O TRP 8 1_555 metalc 2.356 A CA 501 B CA CA 1_555 A GLY 12 A O GLY 12 1_555 metalc 2.404 A CA 501 B CA CA 1_555 A ASP 35 A OD2 ASP 35 1_555 metalc 2.380 A CA 501 B CA CA 1_555 A GLY 10 A O GLY 10 1_555 metalc 2.422 A CA 501 B CA CA 1_555 A ASP 35 A OD1 ASP 35 1_555 metalc 2.293 A CA 501 B CA CA 1_555 A GEL 420 C O4P GEL 1_555 metalc 2.298 A CA 501 B CA CA 1_555 A GEL 420 C O2P GEL 1_555 HYDROLASE HYDROLASE PA2_APIME UNP 1 1 P00630 GSLFLLLLSTSHGWQIRDRIGDNELEERIIYPGTLWCGHGNKSSGPNELGRFKHTDACCRTHDMCPDVMSAGESKHGLTN TASHTRLSCDCDDKFYDCLKNSADTISSYFVGKMYFNLIDTKCYKLEHPVTGCGERTEGRCLHYTVDKSKPKVYQWFDLR KY 29 162 1POC 1 134 P00630 A 1 1 134 2 2 2 2 anti-parallel anti-parallel anti-parallel anti-parallel A VAL 40 A VAL 40 A MET 41 A MET 41 A ARG 58 A ARG 58 A LEU 59 A LEU 59 A SER 46 A SER 46 A LYS 47 A LYS 47 A LEU 50 A LEU 50 A THR 51 A THR 51 A CYS 95 A CYS 95 A GLU 99 A GLU 99 A VAL 125 A VAL 125 A PHE 129 A PHE 129 A VAL 102 A VAL 102 A GLY 104 A GLY 104 A THR 117 A THR 117 A VAL 118 A VAL 118 Unknown 4 BINDING SITE FOR RESIDUE CA A 501 Software 5 BINDING SITE FOR RESIDUE GEL A 420 Software 13 A TRP 8 A TRP 8 4 1_555 A GLY 10 A GLY 10 4 1_555 A GLY 12 A GLY 12 4 1_555 A ASP 35 A ASP 35 4 1_555 A TRP 8 A TRP 8 5 1_555 A GLY 10 A GLY 10 5 1_555 A GLY 12 A GLY 12 5 1_555 A ASP 35 A ASP 35 5 1_555 A GEL 420 C GEL 5 1_555 A ILE 1 A ILE 1 13 1_555 A TRP 8 A TRP 8 13 1_555 A GLY 10 A GLY 10 13 1_555 A HIS 11 A HIS 11 13 1_555 A GLY 12 A GLY 12 13 1_555 A HIS 34 A HIS 34 13 1_555 A ASP 35 A ASP 35 13 1_555 A THR 57 A THR 57 13 1_555 A PHE 67 A PHE 67 13 1_555 A PHE 82 A PHE 82 13 10_665 A MET 86 A MET 86 13 10_665 A TYR 87 A TYR 87 13 1_555 A CA 501 B CA 13 1_555 98 I 41 2 2