Structure of PDB 7qbt Chain D Binding Site BS04

Receptor Information

>7qbt Chain D (length=410) Species: 2214 (Methanosarcina acetivorans)

MEVVVDVGGNPGVDCKGFCKYCYFKKVKDIQPLGCKYCLPFKKGCDYCTR
SVKESYSGFKSLQMVLEETANKLYFTSGEVKKFTVSGGGDLSCYPELKSL
ITFLSQFNTPIHLGYTSGKGFSKPDDALFYIDNGVTEVSFTVFATDPALR
AEYMKDPEPEASIQVLRDFCTHCEVYGAIVLLPGINDGEVLEKTLCDLEN
MGAKGAILMRFANFQENGLILNNSPIIPGITPHTVSEFTEIVRSSAEKHP
SIRITGTPLEDPLIGSPFAIRNVPEALLKLPRVSKKATIITGQVAASRLT
EIFEALGGTVNVIPVKKDIGCLITIDDFKALDLSEVTETVFIPGRAFVHD
MEIKEALRRDGVDRIVRRGPERLSVDGEMSIGMTREEVLELEVENFTELI
GQINSLGLPL

Ligand information

• Ligand ID: COB
• InChI: InChI=1S/C62H88N13O14P.CH3.Co/c1-29-20-39-40(21-30(29)2)75(28-70-39)57-52(84)53(41(27-76)87-57)89-90(85,86)88-31(3)26-69-49(83)18-19-59(8)37(22-46(66)80)56-62(11)61(10,25-48(68)82)36(14-17-45(65)79)51(74-62)33(5)55-60(9,24-47(67)81)34(12-15-43(63)77)38(71-55)23-42-58(6,7)35(13-16-44(64)78)50(72-42)32(4)54(59)73-56;;/h20-21,23,28,31,34-37,41,52-53,57,76,84H,12-19,22,24-27H2,1-11H3,(H2,63,77)(H2,64,78)(H2,65,79)(H2,66,80)(H2,67,81)(H2,68,82)(H,69,83)(H,85,86);1H3;/q;;+1/b42-23-,54-32-,55-33-;;/t31-,34-,35-,36-,37+,41-,52-,53-,57+,59-,60+,61+,62+;;/m1../s1
• InChIKey: BMOGZGJBQIUQJG-BYLSPCLQSA-N
• SMILES:
  : Cc1cc2c(cc1C)n(cn2)[C@@H]3[C@@H]([C@@H]([C@H](O3)CO)O[P@@](=O)(O)O[C@H](C)CNC(=O)CC[C@@]4([C@H](C5=[N-]6C4=C(C7=[N]8[Co+2]69([N]1=C(C=C8C([C@@H]7CCC(=O)N)(C)C)[C@H]([C@](C1=C(C1=[N]9[C@@]5([C@@]([C@@H]1CCC(=O)N)(C)CC(=O)N)C)C)(C)CC(=O)N)CCC(=O)N)C)C)CC(=O)N)C)O
  : C[Co++]|12|3|N4=C5C=C6N|1=C([CH](CCC(N)=O)C6(C)C)C(=C7[N-]2=C([CH](CC(N)=O)[C]7(C)CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]8[CH](O)[CH](O[CH]8CO)n9cnc%10cc(C)c(C)cc9%10)[C]%11(C)N|3=C([CH](CCC(N)=O)[C]%11(C)CC(N)=O)C(=C4[C](C)(CC(N)=O)[CH]5CCC(N)=O)C)C
  OpenEye OEToolkits 1.7.5: Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5=[N-]6C4=C(C7=[N]8[Co+2]69([N]1=C(C=C8C(C7CCC(=O)N)(C)C)C(C(C1=C(C1=[N]9C5(C(C1CCC(=O)N)(C)CC(=O)N)C)C)(C)CC(=O)N)CCC(=O)N)C)C)CC(=O)N)C)O
  : C[Co++]|12|3|N4=C5C=C6N|1=C([C@@H](CCC(N)=O)C6(C)C)C(=C7[N@@-]2=C([C@H](CC(N)=O)[C@@]7(C)CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]8[C@@H](O)[C@H](O[C@@H]8CO)n9cnc%10cc(C)c(C)cc9%10)[C@]%11(C)N|3=C([C@@H](CCC(N)=O)[C@]%11(C)CC(N)=O)C(=C4[C@@](C)(CC(N)=O)[C@@H]5CCC(N)=O)C)C
• Formula: C63 H91 Co N13 O14 P
• Name: CO-METHYLCOBALAMIN
• PDB chain: 7qbt Chain D Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qbt Crystallographic snapshots of a B 12 -dependent radical SAM methyltransferase.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): Y23 F24 Y47 R210 A212 N217 L219 I220 L221 N223 P258 F268 I289 T291 D318 I319 G320 C321 L322 F341 I342 P343 R345 F347 G369 P370 E371 R372 L373 S374 D376 E378
• Binding residue (residue number reindexed from 1): Y23 F24 Y47 R210 A212 N217 L219 I220 L221 N223 P258 F268 I289 T291 D318 I319 G320 C321 L322 F341 I342 P343 R345 F347 G369 P370 E371 R372 L373 S374 D376 E378
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.1.1.379: [methyl coenzyme M reductase]-L-arginine C-5-methyltransferase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008168 methyltransferase activity
• GO:0035244 protein-arginine C-methyltransferase activity
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0032259 methylation
• GO:0043687 post-translational protein modification

External links

• PDB: RCSB:7qbt, PDBe:7qbt, PDBj:7qbt
• PDBsum: 7qbt
• PubMed: 35110733
• UniProt: Q8THG6|MCRAM_METAC [Methyl coenzyme M reductase]-L-arginine C-5-methyltransferase (Gene Name=MA_4551)