Structure of PDB 7npa Chain B Binding Site BS09

Receptor Information

>7npa Chain B (length=618) Species: 523845 (Methanothermococcus thermolithotrophicus DSM 2095)

MYEWKLNDIVDNGICAKCGTCTVVCPNGILTFEDRPKLTEECLRKGNGMC
FEVCPRVSSGKYQIKIREKFKEEYYYGKGDVEGQDGGVVTTFLKYLLKNK
KIDGAIVVGDECWKPVSLIVQNEEDLMNTTKSKYTVSTLEALKTAGEMGL
EKVAVVGLPCQINGLRKLQYFQYLAKHDGELGKNGKPVKLPKIEYLIGLL
CTEKFEYDELKETLAKYNINMDDVEKFDIKKGKLLVYVNGEEHKIPLKEI
ELSAGCKMCRDFDAEMADVSVGCVGSPDGYSTVIIRTEKGEEIKNAIELK
EGVNLEAIEKLRDLKLNRFKKEVERRKAEDEKVSFYWTADYGGVGKRADG
TYFIRIRAKPAGWYSIDEAREILEIAEKYDGKIKMTNRGAFEIHGISGFD
VEAMVLELMEKGFITGSEGPLVRATLACPGEGNCGSGLINTTELCKILED
NFKEHPAPYKFKIAISGCPNKCVRPQIHDIGIAGVKFPVVNEENCNGCGR
CAEVCKIEAIDIRGETSYTNYNVCIGCGKCIKACPNEGRDVKEEGFMVYV
GGKTGREVIEGVSMKLMSVEEILNLIDKVLIVYHKYAKKPQRERLAAVMA
RIGKGKFLEEVKELMEQN

Ligand information

• Ligand ID: SRM
• InChI: InChI=1S/C42H46N4O16.Fe/c1-41(17-39(59)60)23(5-9-35(51)52)29-14-27-21(11-37(55)56)19(3-7-33(47)48)25(43-27)13-26-20(4-8-34(49)50)22(12-38(57)58)28(44-26)15-31-42(2,18-40(61)62)24(6-10-36(53)54)30(46-31)16-32(41)45-29;/h13-16,23-24H,3-12,17-18H2,1-2H3,(H10,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62);/q;+2/p-2/t23?,24-,41+,42+;/m1./s1
• InChIKey: DLKSSIHHLYNIKN-MWBYXLBFSA-L
• SMILES:
  OpenEye OEToolkits 2.0.7: C[C@@]1(C(C2=[N]3C1=Cc4c(c(c5n4[Fe]36N7C(=C5)C(=C(C7=CC8=[N]6C(=C2)[C@@](C8CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
  ACDLabs 10.04: O=C(O)CCC=6C7=Cc1c(c(c2n1[Fe]84N5C(=CC3=C(CCC(=O)O)C(C(=C2)N34)(C)CC(=O)O)C(C(=C5C=C(C=6CC(=O)O)N78)CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O
  OpenEye OEToolkits 2.0.7: CC1(C(C2=[N]3C1=Cc4c(c(c5n4[Fe]36N7C(=C5)C(=C(C7=CC8=[N]6C(=C2)C(C8CCC(=O)O)(C)CC(=O)O)CC(=O)O)CCC(=O)O)CCC(=O)O)CC(=O)O)CCC(=O)O)CC(=O)O
  CACTVS 3.385: C[C@]1(CC(O)=O)[C@@H](CCC(O)=O)C2=NC1=CC3=NC(=Cc4n5[Fe][N@@]6C(=C2)C(=C(CCC(O)=O)C6=Cc5c(CCC(O)=O)c4CC(O)=O)CC(O)=O)[C@@](C)(CC(O)=O)[C@@H]3CCC(O)=O
  CACTVS 3.385: C[C]1(CC(O)=O)[CH](CCC(O)=O)C2=NC1=CC3=NC(=Cc4n5[Fe][N]6C(=C2)C(=C(CCC(O)=O)C6=Cc5c(CCC(O)=O)c4CC(O)=O)CC(O)=O)[C](C)(CC(O)=O)[CH]3CCC(O)=O
• Formula: C42 H44 Fe N4 O16
• Name: SIROHEME
• PDB chain: 7npa Chain B Residue 4210

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7npa Structures of the sulfite detoxifying F 420 -dependent enzyme from Methanococcales.
• Resolution: 1.55 Å
• Binding residue (original residue number in PDB): F353 R355 K384 T386 N387 R388 E392 H394 Y459 K460 K462 K553 T554 G555 R556 R594
• Binding residue (residue number reindexed from 1): F353 R355 K384 T386 N387 R388 E392 H394 Y459 K460 K462 K553 T554 G555 R556 R594
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.8.98.3: sulfite reductase (coenzyme F420).

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0016491 oxidoreductase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding
• GO:0052592 oxidoreductase activity, acting on CH or CH2 groups, with an iron-sulfur protein as acceptor

External links

• PDB: RCSB:7npa, PDBe:7npa, PDBj:7npa
• PDBsum: 7npa
• PubMed: 36658338
• UniProt: A0A2Z5PF12