3VDR - Sequence, Chains, Asymmetric and Biological Units

• Title: CRYSTAL STRUCTURE OF D-3-HYDROXYBUTYRATE DEHYDROGENASE, PREP THE PRESENCE OF THE SUBSTRATE D-3-HYDROXYBUTYRATE AND NAD(+
• Keywords: NAD DEPENDENT ENZYMES, KETONE BODIES, OXIDOREDUCTASE
• Experiment: X-ray diffraction
• Number of Models: 1

Database	ID code	Status	Coordinate files
			Header	Asymmetric unit	Biological unit
PDB	3VDR	released	available	available	Quaternary Structure Server

Asymmetric unit from PDB

Unit	Type	Name	Chain ID	Residues	Atoms	Hetatoms
1	Protein	D-3-HYDROXYBUTYRATE DEHYDROGENASE	A	260	1906	0
2	Protein	D-3-HYDROXYBUTYRATE DEHYDROGENASE	B	260	1906	0
3	Protein	D-3-HYDROXYBUTYRATE DEHYDROGENASE	C	260	1906	0
4	Protein	D-3-HYDROXYBUTYRATE DEHYDROGENASE	D	260	1906	0
5	Ligand	D-3-HYDROXYBUTYRATE DEHYDROGENASE	A	6	0	104
6	Ligand	D-3-HYDROXYBUTYRATE DEHYDROGENASE	B	6	0	104
7	Ligand	D-3-HYDROXYBUTYRATE DEHYDROGENASE	C	4	0	102
8	Ligand	D-3-HYDROXYBUTYRATE DEHYDROGENASE	D	5	0	103
9	Water			244	0	244
total				1305	7624	657

Proteins

Unit 1	MET 1 LEU 2 LYS 3 GLY 4 LYS 5 LYS 6 ALA 7 VAL 8 VAL 9 THR 10 GLY 11 SER 12 THR 13 SER 14 GLY 15 ILE 16 GLY 17 LEU 18 ALA 19 MET 20 ALA 21 THR 22 GLU 23 LEU 24 ALA 25 LYS 26 ALA 27 GLY 28 ALA 29 ASP 30 VAL 31 VAL 32 ILE 33 ASN 34 GLY 35 PHE 36 GLY 37 GLN 38 PRO 39 GLU 40 ASP 41 ILE 42 GLU 43 ARG 44 GLU 45 ARG 46 SER 47 THR 48 LEU 49 GLU 50 SER 51 LYS 52 PHE 53 GLY 54 VAL 55 LYS 56 ALA 57 TYR 58 TYR 59 LEU 60 ASN 61 ALA 62 ASP 63 LEU 64 SER 65 ASP 66 ALA 67 GLN 68 ALA 69 THR 70 ARG 71 ASP 72 PHE 73 ILE 74 ALA 75 LYS 76 ALA 77 ALA 78 GLU 79 ALA 80 LEU 81 GLY 82 GLY 83 LEU 84 ASP 85 ILE 86 LEU 87 VAL 88 ASN 89 ASN 90 ALA 91 GLY 92 ILE 93 GLN 94 HIS 95 THR 96 ALA 97 PRO 98 ILE 99 GLU 100 GLU 101 PHE 102 PRO 103 VAL 104 ASP 105 LYS 106 TRP 107 ASN 108 ALA 109 ILE 110 ILE 111 ALA 112 LEU 113 ASN 114 LEU 115 SER 116 ALA 117 VAL 118 PHE 119 HIS 120 GLY 121 THR 122 ALA 123 ALA 124 ALA 125 LEU 126 PRO 127 ILE 128 MET 129 GLN 130 LYS 131 GLN 132 GLY 133 TRP 134 GLY 135 ARG 136 ILE 137 ILE 138 ASN 139 ILE 140 ALA 141 SER 142 ALA 143 HIS 144 GLY 145 LEU 146 VAL 147 ALA 148 SER 149 VAL 150 ASN 151 LYS 152 SER 153 ALA 154 TYR 155 VAL 156 ALA 157 ALA 158 LYS 159 HIS 160 GLY 161 VAL 162 VAL 163 GLY 164 LEU 165 THR 166 LYS 167 VAL 168 THR 169 ALA 170 LEU 171 GLU 172 ASN 173 ALA 174 GLY 175 LYS 176 GLY 177 ILE 178 THR 179 CYS 180 ASN 181 ALA 182 ILE 183 CYS 184 PRO 185 GLY 186 TRP 187 VAL 188 ARG 189 THR 190 PRO 191 LEU 192 VAL 193 GLU 194 LYS 195 GLN 196 ILE 197 GLU 198 ALA 199 ILE 200 SER 201 GLN 202 GLN 203 LYS 204 GLY 205 ILE 206 ASP 207 ILE 208 GLU 209 ALA 210 ALA 211 ALA 212 ARG 213 GLU 214 LEU 215 LEU 216 ALA 217 GLU 218 LYS 219 GLN 220 PRO 221 SER 222 LEU 223 GLN 224 PHE 225 VAL 226 THR 227 PRO 228 GLU 229 GLN 230 LEU 231 GLY 232 GLY 233 ALA 234 ALA 235 VAL 236 PHE 237 LEU 238 SER 239 SER 240 ALA 241 ALA 242 ALA 243 ASP 244 GLN 245 MET 246 THR 247 GLY 248 THR 249 THR 250 LEU 251 SER 252 LEU 253 ASP 254 GLY 255 GLY 256 TRP 257 THR 258 ALA 259 ARG 260
Unit 2	MET 1 LEU 2 LYS 3 GLY 4 LYS 5 LYS 6 ALA 7 VAL 8 VAL 9 THR 10 GLY 11 SER 12 THR 13 SER 14 GLY 15 ILE 16 GLY 17 LEU 18 ALA 19 MET 20 ALA 21 THR 22 GLU 23 LEU 24 ALA 25 LYS 26 ALA 27 GLY 28 ALA 29 ASP 30 VAL 31 VAL 32 ILE 33 ASN 34 GLY 35 PHE 36 GLY 37 GLN 38 PRO 39 GLU 40 ASP 41 ILE 42 GLU 43 ARG 44 GLU 45 ARG 46 SER 47 THR 48 LEU 49 GLU 50 SER 51 LYS 52 PHE 53 GLY 54 VAL 55 LYS 56 ALA 57 TYR 58 TYR 59 LEU 60 ASN 61 ALA 62 ASP 63 LEU 64 SER 65 ASP 66 ALA 67 GLN 68 ALA 69 THR 70 ARG 71 ASP 72 PHE 73 ILE 74 ALA 75 LYS 76 ALA 77 ALA 78 GLU 79 ALA 80 LEU 81 GLY 82 GLY 83 LEU 84 ASP 85 ILE 86 LEU 87 VAL 88 ASN 89 ASN 90 ALA 91 GLY 92 ILE 93 GLN 94 HIS 95 THR 96 ALA 97 PRO 98 ILE 99 GLU 100 GLU 101 PHE 102 PRO 103 VAL 104 ASP 105 LYS 106 TRP 107 ASN 108 ALA 109 ILE 110 ILE 111 ALA 112 LEU 113 ASN 114 LEU 115 SER 116 ALA 117 VAL 118 PHE 119 HIS 120 GLY 121 THR 122 ALA 123 ALA 124 ALA 125 LEU 126 PRO 127 ILE 128 MET 129 GLN 130 LYS 131 GLN 132 GLY 133 TRP 134 GLY 135 ARG 136 ILE 137 ILE 138 ASN 139 ILE 140 ALA 141 SER 142 ALA 143 HIS 144 GLY 145 LEU 146 VAL 147 ALA 148 SER 149 VAL 150 ASN 151 LYS 152 SER 153 ALA 154 TYR 155 VAL 156 ALA 157 ALA 158 LYS 159 HIS 160 GLY 161 VAL 162 VAL 163 GLY 164 LEU 165 THR 166 LYS 167 VAL 168 THR 169 ALA 170 LEU 171 GLU 172 ASN 173 ALA 174 GLY 175 LYS 176 GLY 177 ILE 178 THR 179 CYS 180 ASN 181 ALA 182 ILE 183 CYS 184 PRO 185 GLY 186 TRP 187 VAL 188 ARG 189 THR 190 PRO 191 LEU 192 VAL 193 GLU 194 LYS 195 GLN 196 ILE 197 GLU 198 ALA 199 ILE 200 SER 201 GLN 202 GLN 203 LYS 204 GLY 205 ILE 206 ASP 207 ILE 208 GLU 209 ALA 210 ALA 211 ALA 212 ARG 213 GLU 214 LEU 215 LEU 216 ALA 217 GLU 218 LYS 219 GLN 220 PRO 221 SER 222 LEU 223 GLN 224 PHE 225 VAL 226 THR 227 PRO 228 GLU 229 GLN 230 LEU 231 GLY 232 GLY 233 ALA 234 ALA 235 VAL 236 PHE 237 LEU 238 SER 239 SER 240 ALA 241 ALA 242 ALA 243 ASP 244 GLN 245 MET 246 THR 247 GLY 248 THR 249 THR 250 LEU 251 SER 252 LEU 253 ASP 254 GLY 255 GLY 256 TRP 257 THR 258 ALA 259 ARG 260
Unit 3	MET 1 LEU 2 LYS 3 GLY 4 LYS 5 LYS 6 ALA 7 VAL 8 VAL 9 THR 10 GLY 11 SER 12 THR 13 SER 14 GLY 15 ILE 16 GLY 17 LEU 18 ALA 19 MET 20 ALA 21 THR 22 GLU 23 LEU 24 ALA 25 LYS 26 ALA 27 GLY 28 ALA 29 ASP 30 VAL 31 VAL 32 ILE 33 ASN 34 GLY 35 PHE 36 GLY 37 GLN 38 PRO 39 GLU 40 ASP 41 ILE 42 GLU 43 ARG 44 GLU 45 ARG 46 SER 47 THR 48 LEU 49 GLU 50 SER 51 LYS 52 PHE 53 GLY 54 VAL 55 LYS 56 ALA 57 TYR 58 TYR 59 LEU 60 ASN 61 ALA 62 ASP 63 LEU 64 SER 65 ASP 66 ALA 67 GLN 68 ALA 69 THR 70 ARG 71 ASP 72 PHE 73 ILE 74 ALA 75 LYS 76 ALA 77 ALA 78 GLU 79 ALA 80 LEU 81 GLY 82 GLY 83 LEU 84 ASP 85 ILE 86 LEU 87 VAL 88 ASN 89 ASN 90 ALA 91 GLY 92 ILE 93 GLN 94 HIS 95 THR 96 ALA 97 PRO 98 ILE 99 GLU 100 GLU 101 PHE 102 PRO 103 VAL 104 ASP 105 LYS 106 TRP 107 ASN 108 ALA 109 ILE 110 ILE 111 ALA 112 LEU 113 ASN 114 LEU 115 SER 116 ALA 117 VAL 118 PHE 119 HIS 120 GLY 121 THR 122 ALA 123 ALA 124 ALA 125 LEU 126 PRO 127 ILE 128 MET 129 GLN 130 LYS 131 GLN 132 GLY 133 TRP 134 GLY 135 ARG 136 ILE 137 ILE 138 ASN 139 ILE 140 ALA 141 SER 142 ALA 143 HIS 144 GLY 145 LEU 146 VAL 147 ALA 148 SER 149 VAL 150 ASN 151 LYS 152 SER 153 ALA 154 TYR 155 VAL 156 ALA 157 ALA 158 LYS 159 HIS 160 GLY 161 VAL 162 VAL 163 GLY 164 LEU 165 THR 166 LYS 167 VAL 168 THR 169 ALA 170 LEU 171 GLU 172 ASN 173 ALA 174 GLY 175 LYS 176 GLY 177 ILE 178 THR 179 CYS 180 ASN 181 ALA 182 ILE 183 CYS 184 PRO 185 GLY 186 TRP 187 VAL 188 ARG 189 THR 190 PRO 191 LEU 192 VAL 193 GLU 194 LYS 195 GLN 196 ILE 197 GLU 198 ALA 199 ILE 200 SER 201 GLN 202 GLN 203 LYS 204 GLY 205 ILE 206 ASP 207 ILE 208 GLU 209 ALA 210 ALA 211 ALA 212 ARG 213 GLU 214 LEU 215 LEU 216 ALA 217 GLU 218 LYS 219 GLN 220 PRO 221 SER 222 LEU 223 GLN 224 PHE 225 VAL 226 THR 227 PRO 228 GLU 229 GLN 230 LEU 231 GLY 232 GLY 233 ALA 234 ALA 235 VAL 236 PHE 237 LEU 238 SER 239 SER 240 ALA 241 ALA 242 ALA 243 ASP 244 GLN 245 MET 246 THR 247 GLY 248 THR 249 THR 250 LEU 251 SER 252 LEU 253 ASP 254 GLY 255 GLY 256 TRP 257 THR 258 ALA 259 ARG 260
Unit 4	MET 1 LEU 2 LYS 3 GLY 4 LYS 5 LYS 6 ALA 7 VAL 8 VAL 9 THR 10 GLY 11 SER 12 THR 13 SER 14 GLY 15 ILE 16 GLY 17 LEU 18 ALA 19 MET 20 ALA 21 THR 22 GLU 23 LEU 24 ALA 25 LYS 26 ALA 27 GLY 28 ALA 29 ASP 30 VAL 31 VAL 32 ILE 33 ASN 34 GLY 35 PHE 36 GLY 37 GLN 38 PRO 39 GLU 40 ASP 41 ILE 42 GLU 43 ARG 44 GLU 45 ARG 46 SER 47 THR 48 LEU 49 GLU 50 SER 51 LYS 52 PHE 53 GLY 54 VAL 55 LYS 56 ALA 57 TYR 58 TYR 59 LEU 60 ASN 61 ALA 62 ASP 63 LEU 64 SER 65 ASP 66 ALA 67 GLN 68 ALA 69 THR 70 ARG 71 ASP 72 PHE 73 ILE 74 ALA 75 LYS 76 ALA 77 ALA 78 GLU 79 ALA 80 LEU 81 GLY 82 GLY 83 LEU 84 ASP 85 ILE 86 LEU 87 VAL 88 ASN 89 ASN 90 ALA 91 GLY 92 ILE 93 GLN 94 HIS 95 THR 96 ALA 97 PRO 98 ILE 99 GLU 100 GLU 101 PHE 102 PRO 103 VAL 104 ASP 105 LYS 106 TRP 107 ASN 108 ALA 109 ILE 110 ILE 111 ALA 112 LEU 113 ASN 114 LEU 115 SER 116 ALA 117 VAL 118 PHE 119 HIS 120 GLY 121 THR 122 ALA 123 ALA 124 ALA 125 LEU 126 PRO 127 ILE 128 MET 129 GLN 130 LYS 131 GLN 132 GLY 133 TRP 134 GLY 135 ARG 136 ILE 137 ILE 138 ASN 139 ILE 140 ALA 141 SER 142 ALA 143 HIS 144 GLY 145 LEU 146 VAL 147 ALA 148 SER 149 VAL 150 ASN 151 LYS 152 SER 153 ALA 154 TYR 155 VAL 156 ALA 157 ALA 158 LYS 159 HIS 160 GLY 161 VAL 162 VAL 163 GLY 164 LEU 165 THR 166 LYS 167 VAL 168 THR 169 ALA 170 LEU 171 GLU 172 ASN 173 ALA 174 GLY 175 LYS 176 GLY 177 ILE 178 THR 179 CYS 180 ASN 181 ALA 182 ILE 183 CYS 184 PRO 185 GLY 186 TRP 187 VAL 188 ARG 189 THR 190 PRO 191 LEU 192 VAL 193 GLU 194 LYS 195 GLN 196 ILE 197 GLU 198 ALA 199 ILE 200 SER 201 GLN 202 GLN 203 LYS 204 GLY 205 ILE 206 ASP 207 ILE 208 GLU 209 ALA 210 ALA 211 ALA 212 ARG 213 GLU 214 LEU 215 LEU 216 ALA 217 GLU 218 LYS 219 GLN 220 PRO 221 SER 222 LEU 223 GLN 224 PHE 225 VAL 226 THR 227 PRO 228 GLU 229 GLN 230 LEU 231 GLY 232 GLY 233 ALA 234 ALA 235 VAL 236 PHE 237 LEU 238 SER 239 SER 240 ALA 241 ALA 242 ALA 243 ASP 244 GLN 245 MET 246 THR 247 GLY 248 THR 249 THR 250 LEU 251 SER 252 LEU 253 ASP 254 GLY 255 GLY 256 TRP 257 THR 258 ALA 259 ARG 260

Ligands

Unit 5	CA 301 CL 302 NAD 303 NAI 304 3HR 305 AAE 306
Unit 6	CA 301 CL 302 NAD 303 NAI 304 3HR 305 AAE 306
Unit 7	NAD 301 NAI 302 3HR 303 AAE 304
Unit 8	CL 301 NAD 302 NAI 303 3HR 304 AAE 305