0.013096 0.007561 0.000000 0.000000 0.015122 0.000000 0.000000 0.000000 0.010925 0.00000 0.00000 0.00000 Chirgadze, N.Y. Schevitz, R.W. Wery, J.-P. http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 12 90.00 90.00 120.00 76.360 76.360 91.530 C22 H24 N2 O4 380.437 4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID non-polymer 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 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 C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking US Nat.Struct.Biol. NSBIEW 2024 1072-8368 2 458 465 10.1038/nsb0695-458 7664108 Structure-based design of the first potent and selective inhibitor of human non-pancreatic secretory phospholipase A2. 1995 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.00000 0.00000 0.00000 298.0 1 IMAGE PLATE 1994-11-03 RIGAKU RAXIS IIC SINGLE WAVELENGTH M x-ray 1 1.54 1.0 1.54 ROTATING ANODE RIGAKU RU200 13945.012 PROTEIN (PHOSPHOLIPASE A2) 3.1.1.4 1 man polymer 40.078 CALCIUM ION 2 syn non-polymer 380.437 4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID 1 syn non-polymer 18.015 water 38 nat water no no NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQ DSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQ DSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC 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 human Homo sample 9606 Homo sapiens 1 2.8 56 VAPOR DIFFUSION 7.0 10 mg/ml of protein; 50 mM buffer (MES or MOPS), 1% pyridine., pH 7.0, VAPOR DIFFUSION, temperature 297K 297 repository Initial release Version format compliance Version format compliance Database references 1 0 1999-11-12 1 1 2008-04-27 1 2 2011-07-13 1 3 2012-02-29 HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8 HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3 RCSB Y RCSB 1999-11-02 REL CA CALCIUM ION 6IN 4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID HOH water CA 198 2 CA CA 198 A CA 199 2 CA CA 199 A 6IN 200 3 6IN 6IN 200 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 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 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 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 342 4 HOH HOH 342 A ASN 1 n 1 ASN 1 A LEU 2 n 2 LEU 2 A VAL 3 n 3 VAL 3 A ASN 4 n 4 ASN 4 A PHE 5 n 5 PHE 5 A HIS 6 n 6 HIS 6 A ARG 7 n 7 ARG 7 A MET 8 n 8 MET 8 A ILE 9 n 9 ILE 9 A LYS 10 n 10 LYS 10 A LEU 11 n 11 LEU 11 A THR 12 n 12 THR 12 A THR 13 n 13 THR 13 A GLY 14 n 14 GLY 14 A LYS 15 n 15 LYS 15 A GLU 16 n 16 GLU 16 A ALA 17 n 17 ALA 17 A ALA 18 n 18 ALA 18 A LEU 19 n 19 LEU 19 A SER 20 n 20 SER 20 A TYR 21 n 21 TYR 21 A GLY 22 n 22 GLY 22 A PHE 23 n 23 PHE 23 A TYR 24 n 24 TYR 24 A GLY 25 n 25 GLY 25 A CYS 26 n 26 CYS 26 A HIS 27 n 27 HIS 27 A CYS 28 n 28 CYS 28 A GLY 29 n 29 GLY 29 A VAL 30 n 30 VAL 30 A GLY 31 n 31 GLY 31 A GLY 32 n 32 GLY 32 A ARG 33 n 33 ARG 33 A GLY 34 n 34 GLY 34 A SER 35 n 35 SER 35 A PRO 36 n 36 PRO 36 A LYS 37 n 37 LYS 37 A ASP 38 n 38 ASP 38 A ALA 39 n 39 ALA 39 A THR 40 n 40 THR 40 A ASP 41 n 41 ASP 41 A ARG 42 n 42 ARG 42 A CYS 43 n 43 CYS 43 A CYS 44 n 44 CYS 44 A VAL 45 n 45 VAL 45 A THR 46 n 46 THR 46 A HIS 47 n 47 HIS 47 A ASP 48 n 48 ASP 48 A CYS 49 n 49 CYS 49 A CYS 50 n 50 CYS 50 A TYR 51 n 51 TYR 51 A LYS 52 n 52 LYS 52 A ARG 53 n 53 ARG 53 A LEU 54 n 54 LEU 54 A GLU 55 n 55 GLU 55 A LYS 56 n 56 LYS 56 A ARG 57 n 57 ARG 57 A GLY 58 n 58 GLY 58 A CYS 59 n 59 CYS 59 A GLY 60 n 60 GLY 60 A THR 61 n 61 THR 61 A LYS 62 n 62 LYS 62 A PHE 63 n 63 PHE 63 A LEU 64 n 64 LEU 64 A SER 65 n 65 SER 65 A TYR 66 n 66 TYR 66 A LYS 67 n 67 LYS 67 A PHE 68 n 68 PHE 68 A SER 69 n 69 SER 69 A ASN 70 n 70 ASN 70 A SER 71 n 71 SER 71 A GLY 72 n 72 GLY 72 A SER 73 n 73 SER 73 A ARG 74 n 74 ARG 74 A ILE 75 n 75 ILE 75 A THR 76 n 76 THR 76 A CYS 77 n 77 CYS 77 A ALA 78 n 78 ALA 78 A LYS 79 n 79 LYS 79 A GLN 80 n 80 GLN 80 A ASP 81 n 81 ASP 81 A SER 82 n 82 SER 82 A CYS 83 n 83 CYS 83 A ARG 84 n 84 ARG 84 A SER 85 n 85 SER 85 A GLN 86 n 86 GLN 86 A LEU 87 n 87 LEU 87 A CYS 88 n 88 CYS 88 A GLU 89 n 89 GLU 89 A CYS 90 n 90 CYS 90 A ASP 91 n 91 ASP 91 A LYS 92 n 92 LYS 92 A ALA 93 n 93 ALA 93 A ALA 94 n 94 ALA 94 A ALA 95 n 95 ALA 95 A THR 96 n 96 THR 96 A CYS 97 n 97 CYS 97 A PHE 98 n 98 PHE 98 A ALA 99 n 99 ALA 99 A ARG 100 n 100 ARG 100 A ASN 101 n 101 ASN 101 A LYS 102 n 102 LYS 102 A THR 103 n 103 THR 103 A THR 104 n 104 THR 104 A TYR 105 n 105 TYR 105 A ASN 106 n 106 ASN 106 A LYS 107 n 107 LYS 107 A LYS 108 n 108 LYS 108 A TYR 109 n 109 TYR 109 A GLN 110 n 110 GLN 110 A TYR 111 n 111 TYR 111 A TYR 112 n 112 TYR 112 A SER 113 n 113 SER 113 A ASN 114 n 114 ASN 114 A LYS 115 n 115 LYS 115 A HIS 116 n 116 HIS 116 A CYS 117 n 117 CYS 117 A ARG 118 n 118 ARG 118 A GLY 119 n 119 GLY 119 A SER 120 n 120 SER 120 A THR 121 n 121 THR 121 A PRO 122 n 122 PRO 122 A ARG 123 n 123 ARG 123 A CYS 124 n 124 CYS 124 A author_defined_assembly 1 monomeric A HIS 27 A O HIS 27 1_555 A CA 198 B CA CA 1_555 A ASP 48 A OD1 ASP 48 1_555 97.2 A HIS 27 A O HIS 27 1_555 A CA 198 B CA CA 1_555 A GLY 31 A O GLY 31 1_555 91.5 A ASP 48 A OD1 ASP 48 1_555 A CA 198 B CA CA 1_555 A GLY 31 A O GLY 31 1_555 89.1 A HIS 27 A O HIS 27 1_555 A CA 198 B CA CA 1_555 A ASP 48 A OD2 ASP 48 1_555 114.4 A ASP 48 A OD1 ASP 48 1_555 A CA 198 B CA CA 1_555 A ASP 48 A OD2 ASP 48 1_555 48.9 A GLY 31 A O GLY 31 1_555 A CA 198 B CA CA 1_555 A ASP 48 A OD2 ASP 48 1_555 131.2 A HIS 27 A O HIS 27 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O40 6IN 1_555 74.9 A ASP 48 A OD1 ASP 48 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O40 6IN 1_555 112.9 A GLY 31 A O GLY 31 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O40 6IN 1_555 155.1 A ASP 48 A OD2 ASP 48 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O40 6IN 1_555 73.8 A HIS 27 A O HIS 27 1_555 A CA 198 B CA CA 1_555 A GLY 29 A O GLY 29 1_555 94.1 A ASP 48 A OD1 ASP 48 1_555 A CA 198 B CA CA 1_555 A GLY 29 A O GLY 29 1_555 168.7 A GLY 31 A O GLY 31 1_555 A CA 198 B CA CA 1_555 A GLY 29 A O GLY 29 1_555 90.4 A ASP 48 A OD2 ASP 48 1_555 A CA 198 B CA CA 1_555 A GLY 29 A O GLY 29 1_555 125.5 A 6IN 200 D O40 6IN 1_555 A CA 198 B CA CA 1_555 A GLY 29 A O GLY 29 1_555 70.3 A HIS 27 A O HIS 27 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 168.8 A ASP 48 A OD1 ASP 48 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 85.4 A GLY 31 A O GLY 31 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 77.7 A ASP 48 A OD2 ASP 48 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 75.5 A 6IN 200 D O40 6IN 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 114.2 A GLY 29 A O GLY 29 1_555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 83.4 A ASN 114 A OD1 ASN 114 1_555 A CA 199 C CA CA 1_555 A TYR 112 A O TYR 112 1_555 91.4 A ASN 114 A OD1 ASN 114 1_555 A CA 199 C CA CA 1_555 A PHE 23 A O PHE 23 1_555 170.1 A TYR 112 A O TYR 112 1_555 A CA 199 C CA CA 1_555 A PHE 23 A O PHE 23 1_555 83.0 A ASN 114 A OD1 ASN 114 1_555 A CA 199 C CA CA 1_555 A GLY 25 A O GLY 25 1_555 81.5 A TYR 112 A O TYR 112 1_555 A CA 199 C CA CA 1_555 A GLY 25 A O GLY 25 1_555 86.2 A PHE 23 A O PHE 23 1_555 A CA 199 C CA CA 1_555 A GLY 25 A O GLY 25 1_555 89.9 A ASN 114 A OD1 ASN 114 1_555 A CA 199 C CA CA 1_555 A HOH 237 E O HOH 12_556 84.6 A TYR 112 A O TYR 112 1_555 A CA 199 C CA CA 1_555 A HOH 237 E O HOH 12_556 155.7 A PHE 23 A O PHE 23 1_555 A CA 199 C CA CA 1_555 A HOH 237 E O HOH 12_556 97.1 A GLY 25 A O GLY 25 1_555 A CA 199 C CA CA 1_555 A HOH 237 E O HOH 12_556 69.5 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 A N SER 71 A N SER 71 A O ARG 74 A O ARG 74 1 A THR 61 -133.79 -72.06 1 A ASP 81 -40.66 154.70 1 A TYR 111 -118.13 52.72 0.24 0.196 0.196 2.80 30.00 209 3933 5.4 87.9 RANDOM 0.001 1000000 1 2.000 2.80 30.00 38 1034 30 0 966 0.010 1.33 24.20 0.736 0.284 0.299 2.93 24 436 8 5.4 94.7 23.60 2.800 30.000 1DB5 4159 0.079 1 14.2000 2.500 97.8 0.274 2.80 2.85 3.3 1 2.50 99.5 data reduction DENZO data scaling SCALEPACK model building X-PLOR refinement X-PLOR 98.0 phasing X-PLOR PHOSPHOLIPASE A2 (E.C.3.1.1.4) HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6 1 N N 2 N N 2 N N 3 N N 4 N N A ASN 1 A ASN 1 HELX_P A GLY 14 A GLY 14 1 1 14 A GLU 16 A GLU 16 HELX_P A GLY 22 A GLY 22 1 2 7 A ASP 38 A ASP 38 HELX_P A ARG 57 A ARG 57 1 3 20 A ASP 81 A ASP 81 HELX_P A ASN 101 A ASN 101 1 4 21 A LYS 102 A LYS 102 HELX_P A TYR 105 A TYR 105 5 5 4 A ASN 106 A ASN 106 HELX_P A GLN 110 A GLN 110 5 6 5 A SER 113 A SER 113 HELX_P A CYS 117 A CYS 117 5 7 5 disulf 2.028 A CYS 26 A SG CYS 26 1_555 A CYS 117 A SG CYS 117 1_555 disulf 2.030 A CYS 28 A SG CYS 28 1_555 A CYS 44 A SG CYS 44 1_555 disulf 2.033 A CYS 43 A SG CYS 43 1_555 A CYS 97 A SG CYS 97 1_555 disulf 2.023 A CYS 49 A SG CYS 49 1_555 A CYS 124 A SG CYS 124 1_555 disulf 2.021 A CYS 50 A SG CYS 50 1_555 A CYS 90 A SG CYS 90 1_555 disulf 2.023 A CYS 59 A SG CYS 59 1_555 A CYS 83 A SG CYS 83 1_555 disulf 2.034 A CYS 77 A SG CYS 77 1_555 A CYS 88 A SG CYS 88 1_555 metalc 2.394 A CA 198 B CA CA 1_555 A HIS 27 A O HIS 27 1_555 metalc 2.530 A CA 198 B CA CA 1_555 A ASP 48 A OD1 ASP 48 1_555 metalc 2.398 A CA 198 B CA CA 1_555 A GLY 31 A O GLY 31 1_555 metalc 2.752 A CA 198 B CA CA 1_555 A ASP 48 A OD2 ASP 48 1_555 metalc 2.559 A CA 198 B CA CA 1_555 A 6IN 200 D O40 6IN 1_555 metalc 2.437 A CA 198 B CA CA 1_555 A GLY 29 A O GLY 29 1_555 metalc 2.555 A CA 198 B CA CA 1_555 A 6IN 200 D O54 6IN 1_555 metalc 2.640 A CA 199 C CA CA 1_555 A ASN 114 A OD1 ASN 114 1_555 metalc 2.548 A CA 199 C CA CA 1_555 A TYR 112 A O TYR 112 1_555 metalc 2.648 A CA 199 C CA CA 1_555 A PHE 23 A O PHE 23 1_555 metalc 2.912 A CA 199 C CA CA 1_555 A GLY 25 A O GLY 25 1_555 metalc 2.773 A CA 199 C CA CA 1_555 A HOH 237 E O HOH 12_556 HYDROLASE/HYDROLASE INHIBITOR S-PLA2; STRUCTURE-BASED DRUG DESIGN, HYDROLASE/HYDROLASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR complex PA2GA_HUMAN UNP 1 P14555 21 144 1DB5 1 124 P14555 A 1 1 124 2 anti-parallel A PHE 68 A PHE 68 A SER 71 A SER 71 A ARG 74 A ARG 74 A CYS 77 A CYS 77 BINDING SITE FOR RESIDUE CA A 198 Software 5 BINDING SITE FOR RESIDUE CA A 199 Software 5 BINDING SITE FOR RESIDUE 6IN A 200 Software 17 A HIS 27 A HIS 27 5 1_555 A GLY 29 A GLY 29 5 1_555 A GLY 31 A GLY 31 5 1_555 A ASP 48 A ASP 48 5 1_555 A 6IN 200 D 6IN 5 1_555 A PHE 23 A PHE 23 5 1_555 A GLY 25 A GLY 25 5 1_555 A TYR 112 A TYR 112 5 1_555 A ASN 114 A ASN 114 5 1_555 A HOH 237 E HOH 5 12_556 A LEU 2 A LEU 2 17 1_555 A HIS 6 A HIS 6 17 1_555 A LEU 19 A LEU 19 17 12_556 A TYR 21 A TYR 21 17 1_555 A HIS 27 A HIS 27 17 1_555 A CYS 28 A CYS 28 17 1_555 A GLY 29 A GLY 29 17 1_555 A VAL 30 A VAL 30 17 1_555 A GLY 31 A GLY 31 17 1_555 A CYS 44 A CYS 44 17 1_555 A HIS 47 A HIS 47 17 1_555 A ASP 48 A ASP 48 17 1_555 A TYR 51 A TYR 51 17 1_555 A LYS 52 A LYS 52 17 1_555 A LYS 62 A LYS 62 17 1_555 A CA 198 B CA 17 1_555 A HOH 236 E HOH 17 1_555 178 P 61 2 2