Structure of PDB 5h8y Chain B Binding Site BS02

Receptor Information

>5h8y Chain B (length=565) Species: 4577 (Zea mays)

KRSKVEIIKEKSNFLRYPLNEELVSEAPNINESAVQLIKFHGSYQQTDRD
VRGQKNYSFMLRTKNPCGKVPNQLYLAMDTLADEFGIGTLRLTTRQTFQL
HGVLKKNLKTVLSTVIKNMGSTLGACGDLNRNVLAPAAPYVKKDILFAQQ
TAENIAALLTPQSGAYYDLWVDEKIMSAEEPPEVTKARNDNSHGTNFPDS
PEPIYGTQYLPRKFKVAVTAAGDNSVDILTNDIGVVVVSDDAGEPIGFNI
YVGGGMGRTHRVETTFPRLADPLGYVPKEDILYAIKAIVVTQRENGRRDD
RKYSRMKYMIDRWGIDRFRAEVEKYYGKKFESFRPLPEWQFNSYLGWQEQ
GDGKLFYGVHVDNGRVGGQAKKTLREIIEKYNLDVSITPNQNLILCGIDQ
AWREPITTALAQAGLLEPKDVDPLNLTAMACPALPLCPLAQTEAERGILP
ILKRIRAVFNKVGIKDSESVVVRITGCPNGCARPYMAELGFVGDGPKSYQ
IWLGGTPNQSTLAESFMDKVKLDDIEKVLEPLFTYWNGTRQEGESFGSFT
NRTGFDKLKEVVNKW

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: 5h8y Chain B Residue 702

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5h8y Structural and mutational studies of an electron transfer complex of maize sulfite reductase and ferredoxin.
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): Y106 Q108 R124 R153 T155 T156 R157 T159 Q161 H163 R275 K276 K278 G318 M319 G320 R368 Q454 P495 C500 L502 N542 G543 C544 R546
• Binding residue (residue number reindexed from 1): Y44 Q46 R62 R91 T93 T94 R95 T97 Q99 H101 R212 K213 K215 G255 M256 G257 R305 Q391 P432 C437 L439 N479 G480 C481 R483
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): R124 R193 K276 K278 P452 C494 C500 C540 C544
• Catalytic site (residue number reindexed from 1): R62 R131 K213 K215 P389 C431 C437 C477 C481
• Enzyme Commision number: 1.8.7.1: assimilatory sulfite reductase (ferredoxin).

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003690 double-stranded DNA binding
• GO:0016002 sulfite reductase activity
• GO:0016491 oxidoreductase activity
• GO:0020037 heme binding
• GO:0046872 metal ion binding
• GO:0050311 sulfite reductase (ferredoxin) activity
• GO:0051536 iron-sulfur cluster binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0000103 sulfate assimilation
• GO:0006790 sulfur compound metabolic process
• GO:0009409 response to cold
• GO:0019418 sulfide oxidation
• GO:0045892 negative regulation of DNA-templated transcription
• GO:1900160 plastid chromosome packaging

Cellular Component

• GO:0009337 sulfite reductase complex (NADPH)
• GO:0009507 chloroplast
• GO:0009570 chloroplast stroma
• GO:0010319 stromule
• GO:0042644 chloroplast nucleoid

External links

• PDB: RCSB:5h8y, PDBe:5h8y, PDBj:5h8y
• PDBsum: 5h8y
• PubMed: 26920048
• UniProt: O23813|SIR_MAIZE Sulfite reductase [ferredoxin], chloroplastic (Gene Name=SIR)