Structure of PDB 5t8s Chain B Binding Site BS01

Receptor Information

>5t8s Chain B (length=376) Species: 242231 (Neisseria gonorrhoeae FA 1090)

SEYLFTSESVSEGHPDKVADQVSDAILDAILAQDPKARVAAETLVNTGLC
VLAGEITTTAQVDYIKVARETIKRIGYNSSELGFDANGCAVGVYYDQQSP
DLNQGAGDQGLMFGYACDETPTLMPFAIYYSHRLMQRQSELRKDGRLPWL
RPDAKAQLTVVYDSETGKVKRIDTVVLSTQHDPAISQEELSKAVIEQIIK
PVLPPELLTDETKYLINPTGRFVIGGPQGDCGLTGRKIIVDTYGGAAPHG
GGAFSGKDPSKVDRSAAYACRYVAKNIVAAGLATQCQIQVSYAIGVAEPT
SISIDTFGTGKISEEKLIALVCEHFDLRPKGIVQMLDLLRPIYGKSAAYG
HFGREEPEFTWERTDKAASLKAAAGL

Ligand information

• Ligand ID: SAM
• InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  ACDLabs 10.04: [O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 5t8s Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5t8s Crystal Structure of a S-adenosylmethionine Synthase from Neisseria gonorrhoeae with bound S-adenosylmethionine, AMP, Pyrophosphate, Phosphate, and Magnesium
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H15 P16 D166 K168 S191 F235 D243
• Binding residue (residue number reindexed from 1): H14 P15 D153 K155 S178 F222 D230
• Annotation score: 5

Enzymatic activity

• Catalytic site (original residue number in PDB): H15 D17 K18 E43 E56 K168 F235 D243 C244 R249 K250 K270 K274 D276
• Catalytic site (residue number reindexed from 1): H14 D16 K17 E42 E55 K155 F222 D230 C231 R236 K237 K257 K261 D263
• Enzyme Commision number: 2.5.1.6: methionine adenosyltransferase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0004478 methionine adenosyltransferase activity
• GO:0005524 ATP binding
• GO:0016740 transferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006556 S-adenosylmethionine biosynthetic process
• GO:0006730 one-carbon metabolic process

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5t8s, PDBe:5t8s, PDBj:5t8s
• PDBsum: 5t8s
• UniProt: Q5FAC0|METK_NEIG1 S-adenosylmethionine synthase (Gene Name=metK)