1YBD - Sequence, Chains, Asymmetric and Biological Units

• Title: CRYSTAL STRUCTURE ANALYSIS OF URIDYLATE KINASE FROM NEISSERI MENINGITIDIS
• Keywords: ALPHA/BETA/ALPHA FOLD, KINASE, HEXAMER, STRUCTURAL GENOMICS, STRUCTURE INITIATIVE, PSI, NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS, NYSGXRC, T1843, TRANSFERASE
• Experiment: X-ray diffraction
• Number of Models: 1

Database	ID code	Status	Coordinate files
			Header	Asymmetric unit	Biological unit
PDB	1YBD	released	available	available	Quaternary Structure Server

Asymmetric unit from PDB

Unit	Type	Name	Chain ID	Residues	Atoms	Hetatoms
1	Protein	URIDYLATE KINASE	A	236	1683	88
2	Protein	URIDYLATE KINASE	B	236	1683	88
3	Protein	URIDYLATE KINASE	C	236	1683	88
4	Ligand	URIDYLATE KINASE	A	2	0	9
5	Ligand	URIDYLATE KINASE	B	1	0	6
6	Ligand	URIDYLATE KINASE	C	1	0	6
7	Water			112	0	112
total				824	5049	397

Proteins

Unit 1	GLN 6 ILE 7 LYS 8 TYR 9 LYS 10 ARG 11 VAL 12 LEU 13 LEU 14 LYS 15 LEU 16 SER 17 GLY 18 GLU 19 SER 20 LEU 21 MSE 22 GLY 23 SER 24 ASP 25 PRO 26 PHE 27 GLY 28 ILE 29 ASN 30 HIS 31 ASP 32 THR 33 ILE 34 VAL 35 GLN 36 THR 37 VAL 38 GLY 39 GLU 40 ILE 41 ALA 42 GLU 43 VAL 44 VAL 45 LYS 46 MSE 47 GLY 48 VAL 49 GLN 50 VAL 51 GLY 52 ILE 53 VAL 54 VAL 55 GLY 56 GLY 57 GLY 58 ASN 59 ILE 60 PHE 61 ARG 62 GLY 63 VAL 64 SER 65 ALA 66 GLN 67 ALA 68 GLY 69 SER 70 MSE 71 ASP 72 ARG 73 ALA 74 THR 75 ALA 76 ASP 77 TYR 78 MSE 79 GLY 80 MSE 81 MSE 82 ALA 83 THR 84 VAL 85 MSE 86 ASN 87 ALA 88 LEU 89 ALA 90 LEU 91 LYS 92 ASP 93 ALA 94 PHE 95 GLU 96 THR 97 LEU 98 GLY 99 ILE 100 LYS 101 ALA 102 ARG 103 VAL 104 GLN 105 SER 106 ALA 107 LEU 108 SER 109 MSE 110 GLN 111 GLN 112 ILE 113 ALA 114 GLU 115 THR 116 TYR 117 ALA 118 ARG 119 PRO 120 LYS 121 ALA 122 ILE 123 GLN 124 TYR 125 LEU 126 GLU 127 GLU 128 GLY 129 LYS 130 VAL 131 VAL 132 ILE 133 PHE 134 ALA 135 ALA 136 GLY 137 THR 138 GLY 139 ASN 140 PRO 141 PHE 142 PHE 143 THR 144 THR 145 ASP 146 THR 147 ALA 148 ALA 149 ALA 150 LEU 151 ARG 152 GLY 153 ALA 154 GLU 155 MSE 156 ASN 157 CYS 158 ASP 159 VAL 160 MSE 161 LEU 162 LYS 163 ALA 164 THR 165 ASN 166 VAL 167 ASP 168 GLY 169 VAL 170 TYR 171 THR 172 ALA 173 ASP 174 PRO 175 LYS 176 LYS 177 ASP 178 PRO 179 SER 180 ALA 181 THR 182 ARG 183 TYR 184 GLU 185 THR 186 ILE 187 THR 188 PHE 189 ASP 190 GLU 191 ALA 192 LEU 193 LEU 194 LYS 195 ASN 196 LEU 197 LYS 198 VAL 199 MSE 200 ASP 201 ALA 202 THR 203 ALA 204 PHE 205 ALA 206 LEU 207 CYS 208 ARG 209 GLU 210 ARG 211 LYS 212 LEU 213 ASN 214 ILE 215 VAL 216 VAL 217 PHE 218 GLY 219 ILE 220 ALA 221 LYS 222 GLU 223 GLY 224 SER 225 LEU 226 LYS 227 ARG 228 VAL 229 ILE 230 THR 231 GLY 232 GLU 233 ASP 234 GLU 235 GLY 236 THR 237 LEU 238 VAL 239 HIS 240 CYS 241
Unit 2	GLN 6 ILE 7 LYS 8 TYR 9 LYS 10 ARG 11 VAL 12 LEU 13 LEU 14 LYS 15 LEU 16 SER 17 GLY 18 GLU 19 SER 20 LEU 21 MSE 22 GLY 23 SER 24 ASP 25 PRO 26 PHE 27 GLY 28 ILE 29 ASN 30 HIS 31 ASP 32 THR 33 ILE 34 VAL 35 GLN 36 THR 37 VAL 38 GLY 39 GLU 40 ILE 41 ALA 42 GLU 43 VAL 44 VAL 45 LYS 46 MSE 47 GLY 48 VAL 49 GLN 50 VAL 51 GLY 52 ILE 53 VAL 54 VAL 55 GLY 56 GLY 57 GLY 58 ASN 59 ILE 60 PHE 61 ARG 62 GLY 63 VAL 64 SER 65 ALA 66 GLN 67 ALA 68 GLY 69 SER 70 MSE 71 ASP 72 ARG 73 ALA 74 THR 75 ALA 76 ASP 77 TYR 78 MSE 79 GLY 80 MSE 81 MSE 82 ALA 83 THR 84 VAL 85 MSE 86 ASN 87 ALA 88 LEU 89 ALA 90 LEU 91 LYS 92 ASP 93 ALA 94 PHE 95 GLU 96 THR 97 LEU 98 GLY 99 ILE 100 LYS 101 ALA 102 ARG 103 VAL 104 GLN 105 SER 106 ALA 107 LEU 108 SER 109 MSE 110 GLN 111 GLN 112 ILE 113 ALA 114 GLU 115 THR 116 TYR 117 ALA 118 ARG 119 PRO 120 LYS 121 ALA 122 ILE 123 GLN 124 TYR 125 LEU 126 GLU 127 GLU 128 GLY 129 LYS 130 VAL 131 VAL 132 ILE 133 PHE 134 ALA 135 ALA 136 GLY 137 THR 138 GLY 139 ASN 140 PRO 141 PHE 142 PHE 143 THR 144 THR 145 ASP 146 THR 147 ALA 148 ALA 149 ALA 150 LEU 151 ARG 152 GLY 153 ALA 154 GLU 155 MSE 156 ASN 157 CYS 158 ASP 159 VAL 160 MSE 161 LEU 162 LYS 163 ALA 164 THR 165 ASN 166 VAL 167 ASP 168 GLY 169 VAL 170 TYR 171 THR 172 ALA 173 ASP 174 PRO 175 LYS 176 LYS 177 ASP 178 PRO 179 SER 180 ALA 181 THR 182 ARG 183 TYR 184 GLU 185 THR 186 ILE 187 THR 188 PHE 189 ASP 190 GLU 191 ALA 192 LEU 193 LEU 194 LYS 195 ASN 196 LEU 197 LYS 198 VAL 199 MSE 200 ASP 201 ALA 202 THR 203 ALA 204 PHE 205 ALA 206 LEU 207 CYS 208 ARG 209 GLU 210 ARG 211 LYS 212 LEU 213 ASN 214 ILE 215 VAL 216 VAL 217 PHE 218 GLY 219 ILE 220 ALA 221 LYS 222 GLU 223 GLY 224 SER 225 LEU 226 LYS 227 ARG 228 VAL 229 ILE 230 THR 231 GLY 232 GLU 233 ASP 234 GLU 235 GLY 236 THR 237 LEU 238 VAL 239 HIS 240 CYS 241
Unit 3	GLN 6 ILE 7 LYS 8 TYR 9 LYS 10 ARG 11 VAL 12 LEU 13 LEU 14 LYS 15 LEU 16 SER 17 GLY 18 GLU 19 SER 20 LEU 21 MSE 22 GLY 23 SER 24 ASP 25 PRO 26 PHE 27 GLY 28 ILE 29 ASN 30 HIS 31 ASP 32 THR 33 ILE 34 VAL 35 GLN 36 THR 37 VAL 38 GLY 39 GLU 40 ILE 41 ALA 42 GLU 43 VAL 44 VAL 45 LYS 46 MSE 47 GLY 48 VAL 49 GLN 50 VAL 51 GLY 52 ILE 53 VAL 54 VAL 55 GLY 56 GLY 57 GLY 58 ASN 59 ILE 60 PHE 61 ARG 62 GLY 63 VAL 64 SER 65 ALA 66 GLN 67 ALA 68 GLY 69 SER 70 MSE 71 ASP 72 ARG 73 ALA 74 THR 75 ALA 76 ASP 77 TYR 78 MSE 79 GLY 80 MSE 81 MSE 82 ALA 83 THR 84 VAL 85 MSE 86 ASN 87 ALA 88 LEU 89 ALA 90 LEU 91 LYS 92 ASP 93 ALA 94 PHE 95 GLU 96 THR 97 LEU 98 GLY 99 ILE 100 LYS 101 ALA 102 ARG 103 VAL 104 GLN 105 SER 106 ALA 107 LEU 108 SER 109 MSE 110 GLN 111 GLN 112 ILE 113 ALA 114 GLU 115 THR 116 TYR 117 ALA 118 ARG 119 PRO 120 LYS 121 ALA 122 ILE 123 GLN 124 TYR 125 LEU 126 GLU 127 GLU 128 GLY 129 LYS 130 VAL 131 VAL 132 ILE 133 PHE 134 ALA 135 ALA 136 GLY 137 THR 138 GLY 139 ASN 140 PRO 141 PHE 142 PHE 143 THR 144 THR 145 ASP 146 THR 147 ALA 148 ALA 149 ALA 150 LEU 151 ARG 152 GLY 153 ALA 154 GLU 155 MSE 156 ASN 157 CYS 158 ASP 159 VAL 160 MSE 161 LEU 162 LYS 163 ALA 164 THR 165 ASN 166 VAL 167 ASP 168 GLY 169 VAL 170 TYR 171 THR 172 ALA 173 ASP 174 PRO 175 LYS 176 LYS 177 ASP 178 PRO 179 SER 180 ALA 181 THR 182 ARG 183 TYR 184 GLU 185 THR 186 ILE 187 THR 188 PHE 189 ASP 190 GLU 191 ALA 192 LEU 193 LEU 194 LYS 195 ASN 196 LEU 197 LYS 198 VAL 199 MSE 200 ASP 201 ALA 202 THR 203 ALA 204 PHE 205 ALA 206 LEU 207 CYS 208 ARG 209 GLU 210 ARG 211 LYS 212 LEU 213 ASN 214 ILE 215 VAL 216 VAL 217 PHE 218 GLY 219 ILE 220 ALA 221 LYS 222 GLU 223 GLY 224 SER 225 LEU 226 LYS 227 ARG 228 VAL 229 ILE 230 THR 231 GLY 232 GLU 233 ASP 234 GLU 235 GLY 236 THR 237 LEU 238 VAL 239 HIS 240 CYS 241

Ligands

Unit 4	GOL 250 FMT 253
Unit 5	GOL 251
Unit 6	GOL 252