Structure of PDB 1ffv Chain B Binding Site BS01

Receptor Information

>1ffv Chain B (length=797) Species: 47421 (Hydrogenophaga pseudoflava)

DAEARELALAGMGASRLRKEDARFIQGKGNYVDDIKMPGMLHMDIVRAPI
AHGRIKKIHKDAALAMPGVHAVLTAEDLKPLKLHWMPTLAGDVAAVLADE
KVHFQMQEVAIVIADDRYIAADAVEAVKVEYDELPVVIDPIDALKPDAPV
LREDLAGKTSGAHGPREHHNHIFTWGAGDKAATDAVFANAPVTVSQHMYY
PRVHPCPLETCGCVASFDPIKGDLTTYITSQAPHVVRTVVSMLSGIPESK
VRIVSPDIGGGFGNKVGIYPGYVCAIVASIVLGRPVKWVEDRVENISTTA
FARDYHMDGELAATPDGKILGLRVNVVADHGAFDACADPTKFPAGLFHIC
SGSYDIPRAHCSVKGVYTNKAPGGVAYRCSFRVTEAVYLIERMVDVLAQK
LNMDKAEIRAKNFIRKEQFPYTTQFGFEYDSGDYHTALKKVLDAVDYPAL
RAEQAARRADPNSPTLMGIGLVTFTEVVGAGPSKMCDILGVGMFDSCEIR
IHPTGSAIARMGTITQGQGHQTTYAQIIATELGIPSEVIQVEEGDTSTAP
YGLGTYGSRSTPVAGAAIALAARKIHAKARKIAAHMLEVNENDLDWEVDR
FKVKGDDSKFKTMADIAWQAYHQPPAGLEPGLEAVHYYDPPNFTYPFGIY
LCVVDIDRATGETKVRRFYALDDCGTRINPMIIEGQIHGGLTEGYAVAMG
QQMPFDAQGNLLGNTLMDYFLPTAVETPHWETDHTVTPSPHHPIGAKGVA
ESPHVGSIPTFTAAVVDAFAHVGVTHLDMPHTSYRVWKSLKEHNLAL

Ligand information

• Ligand ID: PCD
• InChI: InChI=1S/C19H26N8O13P2S2.Mo.H2O.2O/c20-7-1-2-27(19(31)22-7)17-11(29)10(28)5(39-17)3-36-41(32,33)40-42(34,35)37-4-6-12(43)13(44)8-16(38-6)24-14-9(23-8)15(30)26-18(21)25-14;;;;/h1-2,5-6,8,10-11,16-17,23,28-29,43-44H,3-4H2,(H,32,33)(H,34,35)(H2,20,22,31)(H4,21,24,25,26,30);;1H2;;/q;+2;;;/p-2/t5-,6-,8+,10-,11-,16-,17-;;;;/m1..../s1
• InChIKey: YEBYDVFRFUQMER-MQPNXHJTSA-L
• SMILES:
  CACTVS 3.385: O.NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]4Nc5nc(N)nc(O)c5N[C@H]4C6=C3S[Mo](=O)(=O)S6)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 2.0.7: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OCC3C4=C(C5C(O3)Nc6c(c(nc(n6)N)O)N5)S[Mo](=O)(=O)(S4)[OH2])O)O
  CACTVS 3.385: O.NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]4Nc5nc(N)nc(O)c5N[CH]4C6=C3S[Mo](=O)(=O)S6)[CH](O)[CH]2O
  OpenEye OEToolkits 2.0.7: C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3C4=C([C@H]5[C@@H](O3)Nc6c(c(nc(n6)N)O)N5)S[Mo](=O)(=O)(S4)[OH2])O)O
• Formula: C19 H26 Mo N8 O16 P2 S2
• Name: (MOLYBDOPTERIN-CYTOSINE DINUCLEOTIDE-S,S)-DIOXO-AQUA-MOLYBDENUM(V);
  MOLYBDENUM COFACTOR;
  MOCO
• PDB chain: 1ffv Chain B Residue 1920

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1ffv The effect of intracellular molybdenum in Hydrogenophaga pseudoflava on the crystallographic structure of the seleno-molybdo-iron-sulfur flavoenzyme carbon monoxide dehydrogenase.
• Resolution: 2.25 Å
• Binding residue (original residue number in PDB): G266 G267 F268 G269 A382 X384 X385 Q522 G523 Q524 H526 T529 Y562 G563 S564 S566 T567 C680 I684 I689 Q692 K753 G754 V755 A756 E757
• Binding residue (residue number reindexed from 1): G260 G261 F262 G263 A376 X378 X379 Q516 G517 Q518 H520 T523 Y556 G557 S558 S560 T561 C674 I678 I683 Q686 K747 G748 V749 A750 E751
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Q237 V272 P349 I355 R384 C385 E757 S758
• Catalytic site (residue number reindexed from 1): Q231 V266 P343 I349 R378 C379 E751 S752
• Enzyme Commision number: 1.2.5.3: aerobic carbon monoxide dehydrogenase.

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0005507 copper ion binding
• GO:0008805 carbon-monoxide oxygenase activity
• GO:0016491 oxidoreductase activity
• GO:0030151 molybdenum ion binding
• GO:0043885 anaerobic carbon-monoxide dehydrogenase activity
• GO:0046872 metal ion binding

External links

• PDB: RCSB:1ffv, PDBe:1ffv, PDBj:1ffv
• PDBsum: 1ffv
• PubMed: 10966817
• UniProt: P19913|DCML_HYDPS Carbon monoxide dehydrogenase large chain (Gene Name=cutL)