Structure of PDB 8j83 Chain A Binding Site BS01

Receptor Information
>8j83 Chain A (length=911) Species: 272630 (Methylorubrum extorquens AM1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TIAFEFDGQQVEAQETIWAVAKRLGTHIPHLCHKPDPGYRPDGNCRACMV
EIEGERVLAASCKRTPAIGMKVKSATERATKARAMVLELLVADQPERATS
HDPSSHFWVQADVLDVTESRFPAAERWTSDVSHPAMSVNLDACIQCNLCV
RACREVQVNDVIGMAYRAAGSKVVFDFDDPMGGSTCVACGECVQACPTGA
LMPAAYLDANQTRTVYPDREVKSLCPYCGVGCQVSYKVKDERIVYAEGVN
GPANQNRLCVKGRFGFDYVHHPHRLTVPLIRLENVPKDANDQVDPANPWT
HFREATWEEALDRAAGGLKAIRDTNGRKALAGFGSAKGSNEEAYLFQKLV
RLGFGTNNVDHCTRLCHASSVAALMEGLNSGAVTAPFSAALDAEVIVVIG
ANPTVNHPVAATFLKNAVKQRGAKLIIMDPRRQTLSRHAYRHLAFRPGSD
VAMLNAMLNVIVTEGLYDEQYIAGYTENFEALREKIVDFTPEKMASVCGI
DAETLREVARLYARAKSSLIFWGMGVSQHVHGTDNSRCLIALALITGQIG
RPGTGLHPLRGQNNVQGASDAGLIPMVYPDYQSVEKDAVRELFEEFWGQS
LDPQKGLTVVEIMRAIHAGEIRGMFVEGENPAMSDPDLNHARHALAMLDH
LVVQDLFLTETAFHADVVLPASAFAEKAGTFTNTDRRVQIAQPVVAPPGD
ARQDWWIIQELARRLDLDWNYGGPADIFAEMAQVMPSLNNITWERLEREG
AVTYPVDAPDQPGNEIIFYAGFPTESGRAKIVPAAIVPPDEVPDDEFPMV
LSTGRVLEHWHTGSMTRRAGVLDALEPEAVAFMAPKELYRLGLRPGGSMR
LETRRGAVVLKVRSDRDVPIGMIFMPFCYAEAAANLLTNPALDPLGKIPE
FKFCAARVVPA
Ligand information
Ligand IDMGD
InChIInChI=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
InChIKeyVQAGYJCYOLHZDH-ILXWUORBSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=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 1.5.0c1nc2c(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 1.5.0c1nc2c(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 10.04O=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 3.341NC1=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
FormulaC20 H26 N10 O13 P2 S2
Name2-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
ChEMBL
DrugBank
ZINCZINC000195757106
PDB chain8j83 Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8j83 Structure and function relationship of formate dehydrogenases: an overview of recent progress.
Resolution2.4 Å
Binding residue
(original residue number in PDB)
K407 C432 L435 C436 Q598 G698 E699 N700 S704 D725 L726 S742 A743 D774 T873 R875 W880 H881 T882 S884 M885 F947 N955 F971
Binding residue
(residue number reindexed from 1)
K337 C362 L365 C366 Q528 G628 E629 N630 S634 D655 L656 S672 A673 D704 T803 R805 W810 H811 T812 S814 M815 F877 N885 F901
Annotation score1
Enzymatic activity
Enzyme Commision number 1.17.1.9: formate dehydrogenase.
Gene Ontology
Molecular Function
GO:0008863 formate dehydrogenase (NAD+) activity
GO:0016491 oxidoreductase activity
GO:0043546 molybdopterin cofactor binding
GO:0046872 metal ion binding
GO:0051536 iron-sulfur cluster binding
GO:0051537 2 iron, 2 sulfur cluster binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0015942 formate metabolic process
GO:0045333 cellular respiration
Cellular Component
GO:1990204 oxidoreductase complex

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:8j83, PDBe:8j83, PDBj:8j83
PDBsum8j83
PubMed37668215
UniProtC5ATT7

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