SitesBLAST

Comparing RR42_RS28450 FitnessBrowser__Cup4G11:RR42_RS28450 to proteins with known functional sites using BLASTp with E ≤ 0.001.

Found 19 hits to proteins with known functional sites

P00926 D-serine dehydratase; D-serine deaminase; DSD; EC 4.3.1.18 from Escherichia coli (strain K12) (see paper)
47% identity, 94% coverage: 21:451/457 of query aligns to 15:440/442 of P00926

• K118 (= K124) modified: N6-(pyridoxal phosphate)lysine

3ss7X Crystal structure of holo d-serine dehydratase from escherichia coli at 1.55 a resolution (see paper)
47% identity, 94% coverage: 21:451/457 of query aligns to 10:435/437 of 3ss7X

• binding pyridoxal-5'-phosphate: K113 (= K124), N165 (= N180), G274 (= G289), V275 (= V290), G276 (= G291), G278 (≠ A293), P279 (= P294), E379 (= E393), T419 (= T435)

3r0xA Crystal structure of selenomethionine incorporated apo d-serine deaminase from salmonella tyhimurium (see paper)
47% identity, 94% coverage: 21:451/457 of query aligns to 13:438/438 of 3r0xA

• binding sodium ion: C276 (= C288), G277 (= G289), E303 (= E315), S307 (= S319), C309 (= C321), L338 (= L349), V340 (= V351)

5ygrD Crystal structure of plp bound diaminopropionate ammonia lyase from salmonella typhimurium (see paper)
24% identity, 56% coverage: 156:411/457 of query aligns to 92:336/388 of 5ygrD

• binding phosphate ion: T113 (≠ S177), D114 (≠ T178), N116 (= N180), H117 (≠ L181), T327 (≠ G402)

Sites not aligning to the query:

• binding phosphate ion: 38, 67

8y1jA Structure of the pyridoxal 5'-phosphate-dependent (plp) threonine deaminase ilva1 from pseudomonas aeruginosa pao1 (see paper)
25% identity, 52% coverage: 173:408/457 of query aligns to 70:290/502 of 8y1jA

• binding 2-ketobutyric acid: S74 (= S177), H78 (≠ L181)

Sites not aligning to the query:

• binding 2-ketobutyric acid: 50, 336, 337, 338, 340, 341, 358, 448, 449

7nbgDDD structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
26% identity, 52% coverage: 163:401/457 of query aligns to 60:283/310 of 7nbgDDD

• active site: S76 (≠ T178), E202 (= E315), A206 (≠ S319), D208 (≠ C321), G231 (= G348)
• binding calcium ion: E202 (= E315), A206 (≠ S319), D208 (≠ C321)
• binding magnesium ion: N239 (≠ G360)
• binding ortho-xylene: S76 (≠ T178), Q81 (≠ L183), I96 (≠ V198), Y113 (≠ R215)
• binding pyridoxal-5'-phosphate: N78 (= N180), G177 (= G289), G178 (≠ V290), G179 (= G291), G180 (= G292), M181 (≠ A293), G231 (= G348), V232 (≠ L349), E275 (= E393), T277 (≠ S395)

Sites not aligning to the query:

• active site: 53, 304, 305
• binding magnesium ion: 3
• binding pyridoxal-5'-phosphate: 52, 53, 305, 306

3l6bA X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor (see paper)
26% identity, 52% coverage: 163:401/457 of query aligns to 61:284/322 of 3l6bA

• active site: S77 (≠ T178), E203 (= E315), A207 (≠ S319), D209 (≠ C321), G232 (= G348), T278 (≠ S395)
• binding malonate ion: S76 (= S177), S77 (≠ T178), N79 (= N180), H80 (≠ L181), R128 (≠ A229), G232 (= G348)
• binding manganese (ii) ion: E203 (= E315), A207 (≠ S319), D209 (≠ C321)
• binding pyridoxal-5'-phosphate: N79 (= N180), G178 (= G289), G179 (≠ V290), G180 (= G291), G181 (= G292), M182 (≠ A293), V233 (≠ L349), E276 (= E393), T278 (≠ S395)

Sites not aligning to the query:

• active site: 54, 305, 306
• binding malonate ion: 54
• binding pyridoxal-5'-phosphate: 53, 54, 306, 307

7nbhAAA structure of human serine racemase in complex with DSiP fragment Z26781964, XChem fragment screen (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 76:288/320 of 7nbhAAA

• active site: S81 (≠ T178), E207 (= E315), A211 (≠ S319), D213 (≠ C321), G236 (= G348)
• binding calcium ion: E207 (= E315), A211 (≠ S319), D213 (≠ C321)
• binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: S81 (≠ T178), G85 (= G182), Q86 (≠ L183), K111 (= K208), I115 (≠ L212), Y118 (≠ R215), D235 (= D347), P281 (= P394)

Sites not aligning to the query:

• active site: 53, 309, 310
• binding N-[(1H-benzimidazol-2-yl)methyl]furan-2-carboxamide: 313, 314, 315

7nbgAAA structure of human serine racemase in complex with DSiP fragment Z52314092, XChem fragment screen (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 76:288/322 of 7nbgAAA

• active site: S81 (≠ T178), E207 (= E315), A211 (≠ S319), D213 (≠ C321), G236 (= G348)
• binding calcium ion: E207 (= E315), A211 (≠ S319), D213 (≠ C321)
• binding pyridoxal-5'-phosphate: N83 (= N180), G182 (= G289), G183 (≠ V290), G184 (= G291), G185 (= G292), M186 (≠ A293), G236 (= G348), V237 (≠ L349), T282 (≠ S395)
• binding ~{N}-[2-(2-methylphenyl)ethyl]ethanamide: S81 (≠ T178), G85 (= G182), Q86 (≠ L183), I101 (≠ V198), K111 (= K208), I115 (≠ L212), Y118 (≠ R215)

Sites not aligning to the query:

• active site: 53, 309, 310
• binding pyridoxal-5'-phosphate: 52, 53, 310, 311

7nbfAAA structure of human serine racemase in complex with DSiP fragment Z126932614, XChem fragment screen (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 76:288/323 of 7nbfAAA

• active site: S81 (≠ T178), E207 (= E315), A211 (≠ S319), D213 (≠ C321), G236 (= G348)
• binding calcium ion: E207 (= E315), A211 (≠ S319), D213 (≠ C321)
• binding magnesium ion: N244 (≠ G360)
• binding pyridoxal-5'-phosphate: N83 (= N180), G182 (= G289), G183 (≠ V290), G184 (= G291), G185 (= G292), M186 (≠ A293), G236 (= G348), V237 (≠ L349), T282 (≠ S395)

Sites not aligning to the query:

• active site: 53, 309, 310
• binding magnesium ion: 3
• binding pyridoxal-5'-phosphate: 52, 53, 310, 311
• binding 2-[(methylsulfonyl)methyl]-1H-benzimidazole: 21, 22, 23, 24, 26, 27, 46

7nbdAAA structure of human serine racemase in complex with DSiP fragment Z235449082, XChem fragment screen (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 76:288/323 of 7nbdAAA

• active site: S81 (≠ T178), E207 (= E315), A211 (≠ S319), D213 (≠ C321), G236 (= G348)
• binding calcium ion: E207 (= E315), A211 (≠ S319), D213 (≠ C321)
• binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: W272 (= W385), L278 (≠ R391)
• binding magnesium ion: N244 (≠ G360)
• binding pyridoxal-5'-phosphate: N83 (= N180), G182 (= G289), G183 (≠ V290), G184 (= G291), G185 (= G292), M186 (≠ A293), G236 (= G348), V237 (≠ L349), E280 (= E393), T282 (≠ S395)

Sites not aligning to the query:

• active site: 53, 309, 310
• binding [4-(1H-benzimidazol-1-yl)phenyl]methanol: 314, 316
• binding magnesium ion: 3
• binding pyridoxal-5'-phosphate: 52, 53, 310, 311

7nbcCCC structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 76:288/323 of 7nbcCCC

• active site: S81 (≠ T178), E207 (= E315), A211 (≠ S319), D213 (≠ C321), G236 (= G348)
• binding biphenyl-4-ylacetic acid: T78 (≠ V175), H79 (≠ G176), H84 (≠ L181), V148 (= V246), H149 (≠ D247), P150 (≠ D248)
• binding calcium ion: E207 (= E315), A211 (≠ S319), D213 (≠ C321)
• binding pyridoxal-5'-phosphate: N83 (= N180), G182 (= G289), G183 (≠ V290), G184 (= G291), G185 (= G292), M186 (≠ A293), G236 (= G348), V237 (≠ L349), T282 (≠ S395)

Sites not aligning to the query:

• active site: 53, 309, 310
• binding pyridoxal-5'-phosphate: 52, 53, 310, 311

7nbcAAA structure of human serine racemase in complex with DSiP fragment Z2856434779, XChem fragment screen (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 76:288/323 of 7nbcAAA

• active site: S81 (≠ T178), E207 (= E315), A211 (≠ S319), D213 (≠ C321), G236 (= G348)
• binding calcium ion: E207 (= E315), A211 (≠ S319), D213 (≠ C321)
• binding magnesium ion: N244 (≠ G360)
• binding pyridoxal-5'-phosphate: N83 (= N180), G182 (= G289), G183 (≠ V290), G184 (= G291), G185 (= G292), M186 (≠ A293), G236 (= G348), V237 (≠ L349), T282 (≠ S395)

Sites not aligning to the query:

• active site: 53, 309, 310
• binding magnesium ion: 3
• binding pyridoxal-5'-phosphate: 52, 53, 310, 311

Q9GZT4 Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 5.1.1.18; EC 4.3.1.18; EC 4.3.1.17 from Homo sapiens (Human) (see 4 papers)
25% identity, 50% coverage: 173:401/457 of query aligns to 79:291/340 of Q9GZT4

• T81 (≠ V175) binding Ca(2+)
• N86 (= N180) binding pyridoxal 5'-phosphate
• Q89 (≠ L183) binding ATP
• Y121 (≠ R215) binding ATP
• D178 (= D277) binding Mg(2+)
• G185 (= G289) binding pyridoxal 5'-phosphate
• G186 (≠ V290) binding pyridoxal 5'-phosphate
• G187 (= G291) binding pyridoxal 5'-phosphate
• G188 (= G292) binding pyridoxal 5'-phosphate
• M189 (≠ A293) binding pyridoxal 5'-phosphate
• E210 (= E315) binding Ca(2+); binding Mg(2+); binding Mn(2+)
• A214 (≠ S319) binding Ca(2+); binding Mg(2+); binding Mn(2+)
• D216 (≠ C321) binding Ca(2+); binding Mg(2+); binding Mn(2+)
• N247 (≠ G360) binding Ca(2+); binding Mg(2+)
• K279 (≠ G389) binding ATP

Sites not aligning to the query:

• 13 binding Mg(2+)
• 31 binding ATP
• 32 binding ATP
• 33 binding ATP
• 51 binding ATP
• 52 binding ATP
• 56 modified: N6-(pyridoxal phosphate)lysine
• 69 binding Ca(2+)
• 313 binding pyridoxal 5'-phosphate
• 316 binding ATP

6zspAAA serine racemase bound to atp and malonate. (see paper)
25% identity, 50% coverage: 173:401/457 of query aligns to 69:281/320 of 6zspAAA

• active site: S74 (≠ T178), E200 (= E315), A204 (≠ S319), D206 (≠ C321), G229 (= G348)
• binding adenosine-5'-triphosphate: Q79 (≠ L183), Y111 (≠ R215), E266 (≠ R386), R267 (≠ T387), K269 (≠ G389)
• binding magnesium ion: E200 (= E315), A204 (≠ S319), D206 (≠ C321)
• binding malonate ion: S73 (= S177), S74 (≠ T178), N76 (= N180), H77 (≠ L181), R125 (≠ A229), G229 (= G348), S232 (= S355)

Sites not aligning to the query:

• active site: 53, 302, 303
• binding adenosine-5'-triphosphate: 28, 29, 30, 48, 49, 306
• binding malonate ion: 53

5ygrB Crystal structure of plp bound diaminopropionate ammonia lyase from salmonella typhimurium (see paper)
25% identity, 42% coverage: 177:368/457 of query aligns to 102:309/365 of 5ygrB