Structure of PDB 7kdy Chain B Binding Site BS02

Receptor Information

>7kdy Chain B (length=664) Species: 2689386 (Streptomyces tokunonensis)

GRKVYFVGLNEYPFLPLVAGLLRTYAEQDERIAAAYDFQEPVFLVAPVQE
MADGIVEPDVLALSCYVWNFRRQMKVAKLVKERYPNVLVVAGGPHVPDRP
GNFFEKHPYVDVLAHGEGEVAFRELLATRLSDHPDYTAVPGVSVRRGTEA
VVGPKAKRLPRLIDTPSPYLLGVMDGAVATCRERGLRFYALWETNRGCPY
SCSFCDWGSATMSTLRKFEDERLQDEIEWFARHDVEDLFICDANFGIMPR
DLEIAHALAEARGELGAPRQVRVNFAKNSNDRVFDISKTWHDADLLMGTT
LSMQSTDMDVLEAIDRKNIGLDNYRKLQQRYAAENIHTYTELILGLPMET
ARSFRDGIGSLLEAGNHEDLRVYELGILPNAPLNTPEKIEQYGLRTVPKR
MYVERPGTPDDEAETFEMVMETNAMPRDAWVESFSFIQAVQFLHNGCYTR
YLSIFLRQEHGIGYTRFYEGLQDYFTGRPDTVLGALYLRMRSLYHDYIDM
PALPLANLVASQPDMAADLAPYGRRRGWTIDNWGWLRIATDFDRFHTELR
EYLATLGLDPAGDARLEDVLRFQQDVMLRPDYSPELGKSAEYAHDWPGYF
AGGLLRPRRVRVAYGDQSFGANGRYRPVPGDLKAFTMAAIGTSYPVSRMG
HFCHRFESAEVTSL

Ligand information

• Ligand ID: B12
• InChI: InChI=1S/C62H90N13O14P.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;/h20-21,23,28,31,34-37,41,52-53,56-57,72,76,84H,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);/q;+2/b42-23-,50-32-,55-33-;/t31-,34-,35-,36-,37+,41-,52-,53-,56-,57+,59-,60+,61+,62+;/m1./s1
• InChIKey: LKVIQTCSMMVGFU-DWSMJLPVSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)OC(C)CNC(=O)CCC4(C(C5C6(C(C(C7=[N]6[Co+2]89[N]5=C4C(=C1[NH]8C(=CC2=[N]9C(=C7C)C(C2CCC(=O)N)(C)CC(=O)N)C(C1CCC(=O)N)(C)C)C)CCC(=O)N)(C)CC(=O)N)C)CC(=O)N)C)O
  CACTVS 3.370: [Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C](C)([CH]8N|3=C(C(=C4[CH](CCC(N)=O)C5(C)C)C)[C](C)(CCC(=O)NC[CH](C)O[P](O)(=O)O[CH]9[CH](O)[CH](O[CH]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[CH]8CC(N)=O)[C](C)(CC(N)=O)[CH]7CCC(N)=O)[C](C)(CC(N)=O)[CH]6CCC(N)=O
  CACTVS 3.370: [Co++]|1|2|3|N4C5=CC6=N|1C(=C(C)C7=N|2[C@@](C)([C@@H]8N|3=C(C(=C4[C@@H](CCC(N)=O)C5(C)C)C)[C@](C)(CCC(=O)NC[C@@H](C)O[P](O)(=O)O[C@H]9[C@@H](O)[C@H](O[C@@H]9CO)n%10cnc%11cc(C)c(C)cc%10%11)[C@H]8CC(N)=O)[C@@](C)(CC(N)=O)[C@@H]7CCC(N)=O)[C@@](C)(CC(N)=O)[C@@H]6CCC(N)=O
• Formula: C62 H89 Co N13 O14 P
• Name: COBALAMIN
• PDB chain: 7kdy Chain B Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7kdy Structure of a B 12 -dependent radical SAM enzyme in carbapenem biosynthesis.
• Resolution: 1.939 Å
• Binding residue (original residue number in PDB): N18 F22 V26 L30 L71 S72 Y74 V75 W76 G100 G101 P102 G124 E125 G126 E127 L199 E201 D214 W215 G216 F247 C249 L386
• Binding residue (residue number reindexed from 1): N10 F14 V18 L22 L63 S64 Y66 V67 W68 G92 G93 P94 G116 E117 G118 E119 L191 E193 D206 W207 G208 F239 C241 L378
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008168 methyltransferase activity
• GO:0031419 cobalamin binding
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0032259 methylation

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:7kdy, PDBe:7kdy, PDBj:7kdy
• PDBsum: 7kdy
• PubMed: 35110734
• UniProt: A0A6B9HEI0