Structure of PDB 6ebz Chain D Binding Site BS01

Receptor Information

>6ebz Chain D (length=313)

KNYYDRSVSPVEYAYFDQSQNMRAINWNKIVDEKDLEVWNRVTQNFWLPE
NIPVSNDLPSWNELDDDWQQLITRTFTGLTLLDTVQSSIGDVAQIKNSLT
EQEQVIYANFAFMVGVHARSFGTIFSTLCTSEQIEEAHEWVVDNEALQAR
PKALIPFYTADDPLKSKIAAALMPGFLLYGGFYLPFYLSARGKLPNTSDI
IRLILRDKVIHNFYSGYKYQLKVAKLSPEKQAEMKQFVFDLLDKMIGLEK
TYLHQLYDGFGLADEAIRFSLYNAGKFLQNLGYESPFTKEETRIAPEVFA
QLSARADENHDFF

Ligand information

• Ligand ID: CA
• InChI: InChI=1S/Ca/q+2
• InChIKey: BHPQYMZQTOCNFJ-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: [Ca++]
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Ca+2]
• Formula: Ca
• Name: CALCIUM ION
• DrugBank: DB14577
• PDB chain: 6ebz Chain D Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6ebz Metal-free class Ie ribonucleotide reductase from pathogens initiates catalysis with a tyrosine-derived dihydroxyphenylalanine radical.
• Resolution: 1.66 Å
• Binding residue (original residue number in PDB): G263 D266 E267
• Binding residue (residue number reindexed from 1): G261 D264 E265
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 1.17.4.1: ribonucleoside-diphosphate reductase.

Gene Ontology

Molecular Function

• GO:0004748 ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0009263 deoxyribonucleotide biosynthetic process

Cellular Component

• GO:0005971 ribonucleoside-diphosphate reductase complex
• GO:0016020 membrane

External links

• PDB: RCSB:6ebz, PDBe:6ebz, PDBj:6ebz
• PDBsum: 6ebz
• PubMed: 30224458
• UniProt: F2I8X9