Structure of PDB 6tg9 Chain A Binding Site BS02

Receptor Information

>6tg9 Chain A (length=949) Species: 1415161 (Rhodobacter capsulatus Y262)

PPLDWTQDMGTPKREGAPVHLTIDGVEVTVPAGTSVLRAAAEAGISIPKL
CATDNVEPVGSCRLCMVEIEGMRGTPTSCTTPVAPGMRVHTQTPQLQKLR
RGVMELYISDHPLDCLTCAANGDCELQDMAGAVGLREVRYQAKDTHFARR
DATGPNPRYIPKDNSNPYFSYDPAKCIVCMRCVRACEEVQGTFALTVMGR
GFDARISPAAPDFLSSDCVSCGACVQACPTATLVEKSVERIGTPERKVVT
TCAYCGVGCSFEAHMLGDQLVRMVPWKGGAANRGHSCVKGRFAYGYATHQ
DRILKPMIRDKITDPWREVNWTEALDFTATRLRALRDSHGADALGVITSS
RCTNEETYLVQKLARAVFGTNNTDTCARVCHSPTGYGLKQTFGTSAGTQD
FDSVEETDLALVIGANPTDGHPVFASRLRKRLRAGAKLIVVDPRRIDLLN
TPHRGEAWHLQLKPGTNVAVMTAMAHVIVTEQIFDKRFIGDRCDWDEWAD
YAEFVANPEYAPEAVESLTGVPAGLLRQAARAYAAAPNAAIYYGLGVTEH
SQGSTTVIAIANLAMMTGNIGRPGVGVNPLRGQNNVQGSCDMGSFPHEFP
GYRHVSDDATRGLFERTWGVTLSSEPGLRIPNMLDAAVEGRFKALYVQGE
DILQSDPDTRHVSAGLAAMDLVIVHDLFLNETANYAHVFLPGSTFLEKDG
TFTNAERRINRVRRVMAPKAGFADWEVTQMLANALGAGWHYTHPSEIMAE
IAATTPGFAAVTYEMLDARGSVQWPCNEKAPEGSPIMHVEGFVRGKGRFI
RTAYLPTDEKTGPRFPLLLTTGRILSQYNVGAQTRRTENTVWHGEDRLEI
HPTDAETRGIRDGDWVRLASRAGETTLRATVTDRVSPGVVYTTFHHPDTQ
ANVVTTDTSDWATNCPEYKVTAVQVAASNGPSDWQQDYAAQAAAARRIE

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: 6tg9 Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6tg9 Cryo-EM structures reveal intricate Fe-S cluster arrangement and charging in Rhodobacter capsulatus formate dehydrogenase.
• Resolution: 3.24 Å
• Binding residue (original residue number in PDB): C261 K295 G420 A421 D425 G426 H427 P449 R450 P470 N473 L551 G552 H556 G588 Q589 T826 R829 I830 L831 K925
• Binding residue (residue number reindexed from 1): C255 K289 G414 A415 D419 G420 H421 P443 R444 P464 N467 L545 G546 H550 G582 Q583 T820 R823 I824 L825 K919
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K295 C386 H387 L551 G588 Q589
• Catalytic site (residue number reindexed from 1): K289 C380 H381 L545 G582 Q583
• 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

External links

• PDB: RCSB:6tg9, PDBe:6tg9, PDBj:6tg9
• PDBsum: 6tg9
• PubMed: 32313256
• UniProt: D5AQH0