Structure of PDB 1fdi Chain A Binding Site BS03

Receptor Information

>1fdi Chain A (length=715) Species: 562 (Escherichia coli)

MKKVVTVCPYCASGCKINLVVDNGKIVRAEAAQGKTNQGTLCLKGYYGWD
FINDTQILTPRLKTPMIRRQRGGKLEPVSWDEALNYVAERLSAIKEKYGP
DAIQTTGSSRGTGNETNYVMQKFARAVIGTNNVDCCARVCHGPSVAGLHQ
SVGNGAMSNAINEIDNTDLVFVFGYNPADSHPIVANHVINAKRNGAKIIV
CDPRKIETARIADMHIALKNGSNIALLNAMGHVIIEENLYDKAFVASRTE
GFEEYRKIVEGYTPESVEDITGVSASEIRQAARMYAQAKSAAILWGMGVT
QFYQGVETVRSLTSLAMLTGNLGKPHAGVNPVRGQNNVQGACDMGALPDT
YPGYQYVKDPANREKFAKAWGVESLPAHTGYRISELPHRAAHGEVRAAYI
MGEDPLQTDAELSAVRKAFEDLELVIVQDIFMTKTASAADVILPSTSWGE
HEGVFTAADRGFQRFFKAVEPKWDLKTDWQIISEIATRMGYPMHYNNTQE
IWDELRHLCPDFYGATYEKMGELGFIQWPCRDTSDADQGTSYLFKEKFDT
PNGLAQFFTCDWVAPIDKLTDEYPMVLSTVREVGHYSCRSMTGNCAALAA
LADEPGYAQINTEDAKRLGIEDEALVWVHSRKGKIITRAQVSDRPNKGAI
YMTYQWWIGACNELVTENLSPITKTPEYKYCAVRVEPIADQRAAEQYVID
EYNKLKTRLREAALA

Ligand information

• Ligand ID: MGD
• InChI: InChI=1S/C20H26N10O13P2S2/c21-19-26-13-7(15(33)28-19)24-6-12(47)11(46)5(41-17(6)25-13)2-40-45(37,38)43-44(35,36)39-1-4-9(31)10(32)18(42-4)30-3-23-8-14(30)27-20(22)29-16(8)34/h3-6,9-10,17-18,24,31-32,46-47H,1-2H2,(H,35,36)(H,37,38)(H3,22,27,29,34)(H4,21,25,26,28,33)/t4-,5-,6+,9-,10-,17-,18-/m1/s1
• InChIKey: VQAGYJCYOLHZDH-ILXWUORBSA-N
• SMILES:
  CACTVS 3.341: NC1=NC2=C(N[CH]3[CH](N2)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
  OpenEye OEToolkits 1.5.0: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(=C(C5C(O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
  OpenEye OEToolkits 1.5.0: c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]4C(=C([C@H]5[C@@H](O4)NC6=C(N5)C(=O)NC(=N6)N)S)S)O)O)N=C(NC2=O)N
  ACDLabs 10.04: O=C1C=2NC3C(S)=C(S)C(OC3NC=2N=C(N)N1)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c5N=C(N)NC4=O)C(O)C6O
  CACTVS 3.341: NC1=NC2=C(N[C@@H]3[C@H](N2)O[C@H](CO[P@@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)C(=C3S)S)C(=O)N1
• Formula: C20 H26 N10 O13 P2 S2
• Name: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE;
  MOLYBDOPTERIN GUANOSINE DINUCLEOTIDE
• ZINC: ZINC000195757106
• PDB chain: 1fdi Chain A Residue 801

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1fdi Crystal structure of formate dehydrogenase H: catalysis involving Mo, molybdopterin, selenocysteine, and an Fe4S4 cluster.
• Resolution: 2.9 Å
• Binding residue (original residue number in PDB): R110 G111 V139 U140 Q335 G402 E403 T408 Q428 D429 I430 S445 D478 T579 R581 C588 Y654 N662 Y678
• Binding residue (residue number reindexed from 1): R110 G111 V139 U140 Q335 G402 E403 T408 Q428 D429 I430 S445 D478 T579 R581 C588 Y654 N662 Y678
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): C11 L41 C42 K44 S108 R110 D134 C140 H141 S180 M297 R333 G334 Q335
• Catalytic site (residue number reindexed from 1): C11 L41 C42 K44 S108 R110 D134 C140 H141 S180 M297 R333 G334 Q335
• Enzyme Commision number: 1.17.98.4: formate dehydrogenase (acceptor).

Gene Ontology

Molecular Function

• GO:0003954 NADH dehydrogenase activity
• GO:0005515 protein binding
• GO:0008863 formate dehydrogenase (NAD+) activity
• GO:0016491 oxidoreductase activity
• GO:0016903 oxidoreductase activity, acting on the aldehyde or oxo group of donors
• GO:0043546 molybdopterin cofactor binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006007 glucose catabolic process
• GO:0009061 anaerobic respiration
• GO:0015942 formate metabolic process
• GO:0015944 formate oxidation
• GO:0019628 urate catabolic process
• GO:0019645 anaerobic electron transport chain
• GO:0045333 cellular respiration

Cellular Component

• GO:0005829 cytosol
• GO:0009326 formate dehydrogenase complex
• GO:0016020 membrane
• GO:0045271 respiratory chain complex I
• GO:1990204 oxidoreductase complex

External links

• PDB: RCSB:1fdi, PDBe:1fdi, PDBj:1fdi
• PDBsum: 1fdi
• PubMed: 9036855
• UniProt: P07658|FDHF_ECOLI Formate dehydrogenase H (Gene Name=fdhF)