Structure of PDB 6yj4 Chain n Binding Site BS01

Receptor Information

>6yj4 Chain n (length=108) Species: 4952 (Yarrowia lipolytica)

SHPVPFSAANKKLVTSMYRQSLKLARNWISNRQLFRQKAVEIRHKFDQNA
QISNPRLLARTLDETRAHLYEFRHPDPIVPPSFPGGTKYERNVPPRMEKI
MQHNLYEP

Ligand information

• Ligand ID: EHZ
• InChI: InChI=1S/C25H49N2O9PS/c1-4-5-6-7-8-9-10-11-12-13-20(28)18-22(30)38-17-16-26-21(29)14-15-27-24(32)23(31)25(2,3)19-36-37(33,34)35/h20,23,28,31H,4-19H2,1-3H3,(H,26,29)(H,27,32)(H2,33,34,35)/t20-,23-/m0/s1
• InChIKey: JYSKQPQRUCZFIQ-REWPJTCUSA-N
• SMILES:
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCCC(CC(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O)O
  CACTVS 3.385: CCCCCCCCCCC[CH](O)CC(=O)SCCNC(=O)CCNC(=O)[CH](O)C(C)(C)CO[P](O)(O)=O
  CACTVS 3.385: CCCCCCCCCCC[C@H](O)CC(=O)SCCNC(=O)CCNC(=O)[C@H](O)C(C)(C)CO[P](O)(O)=O
  OpenEye OEToolkits 2.0.6: CCCCCCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O)O
• Formula: C25 H49 N2 O9 P S
• Name: ~{S}-[2-[3-[[(2~{R})-3,3-dimethyl-2-oxidanyl-4-phosphonooxy-butanoyl]amino]propanoylamino]ethyl] (3~{S})-3-oxidanyltetradecanethioate
• PDB chain: 6yj4 Chain U Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6yj4 Mitochondrial complex I structure reveals ordered water molecules for catalysis and proton translocation.
• Resolution: 2.7 Å
• Binding residue (original residue number in PDB): P6 N11 F47 N50 L59 T62 T66
• Binding residue (residue number reindexed from 1): P5 N10 F46 N49 L58 T61 T65
• Annotation score: 1

Gene Ontology

Biological Process

• GO:0006120 mitochondrial electron transport, NADH to ubiquinone

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0045271 respiratory chain complex I

External links

• PDB: RCSB:6yj4, PDBe:6yj4, PDBj:6yj4
• PDBsum: 6yj4
• PubMed: 32747785
• UniProt: Q6C9Z1