Structure of PDB 7qbu Chain A Binding Site BS04

Receptor Information

>7qbu Chain A (length=418) Species: 2214 (Methanosarcina acetivorans)

ENLYFQGHMEVVVDVGGNPGVDCKGFCKYCYFKKVKDIQPLGCKYCLPFK
KGCDYCTRSVKESYSGFKSLQMVLEETANKLYFTSGEVKKFTVSGGGDLS
CYPELKSLITFLSQFNTPIHLGYTSGKGFSKPDDALFYIDNGVTEVSFTV
FATDPALRAEYMKDPEPEASIQVLRDFCTHCEVYGAIVLLPGINDGEVLE
KTLCDLENMGAKGAILMRFANFQENGLILNNSPIIPGITPHTVSEFTEIV
RSSAEKHPSIRITGTPLEDPLIGSPFAIRNVPEALLKLPRVSKKATIITG
QVAASRLTEIFEALGGTVNVIPVKKDIGCLITIDDFKALDLSEVTETVFI
PGRAFVHDMEIKEALRRDGVDRIVRRGPERLSVDGEMSIGMTREEVLELE
VENFTELIGQINSLGLPL

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: 7qbu Chain A Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7qbu Crystallographic snapshots of a B 12 -dependent radical SAM methyltransferase.
• Resolution: 2.298 Å
• Binding residue (original residue number in PDB): Y23 F24 Y47 R210 A212 N217 L219 I220 L221 N223 P258 P267 F268 I289 T291 D318 I319 G320 C321 L322 F341 P343 R345 F347 G369 P370 E371 R372 L373 S374
• Binding residue (residue number reindexed from 1): Y31 F32 Y55 R218 A220 N225 L227 I228 L229 N231 P266 P275 F276 I297 T299 D326 I327 G328 C329 L330 F349 P351 R353 F355 G377 P378 E379 R380 L381 S382
• 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:7qbu, PDBe:7qbu, PDBj:7qbu
• PDBsum: 7qbu
• PubMed: 35110733
• UniProt: Q8THG6|MCRAM_METAC [Methyl coenzyme M reductase]-L-arginine C-5-methyltransferase (Gene Name=MA_4551)