Structure of PDB 5r1r Chain A Binding Site BS01

Receptor Information
>5r1r Chain A (length=738) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MNQNLLVTKRDGSTERINLDKIHRVLDWAAEGLHNVSISQVELRSHIQFY
DGIKTSDIHETIIKAAADLISRDAPDYQYLAARLAIFHLRKKAYGQFEPP
ALYDHVVKMVEMGKYDNHLLEDYTEEEFKQMDTFIDHDRDMTFSYAAVKQ
LEGKYLVQNRVTGEIYESAQFLYILVAACLFSNYPRETRLQYVKRFYDAV
STFKISLPTPIMSGVRTPTRQFSSCVLIECGDSLDSINATSSAIVKYVSQ
RAGIGINAGRIRALGSPIRGGEAFHTGCIPFYKHFQTAVKSCSQGGVRGG
AATLFYPMWHLEVESLLVLKNNRGVEGNRVRHMDYGVQINKLMYTRLLKG
EDITLFSPSDVPGLYDAFFADQEEFERLYTKYEKDDSIRKQRVKAVELFS
LMMQERASTGRIYIQNVDHCNTHSPFDPAIAPVRQSNLCLAIALPTKPLN
DVNDENGEIALCTLSAFNLGAINNLDELEELAILAVRALDALLDYQDYPI
PAAKRGAMGRRTLGIGVINFAYYLAKHGKRYSDGSANNLTHKTFEAIQYY
LLKASNELAKEQGACPWFNETTYAKGILPIDTYKKDLDTIANEPLHYDWE
ALRESIKTHGLRNSTLSALMPSETSSQISNATNGIEPPRGYVSIKASKDG
ILRQVVPDYEHLHDAYELLWEMPGNDGYLQLVGIMQKFIDQSISANTNYD
PSRFPSGKVPMQQLLKDLLTAYKFGVKTLYYQNTRDGA
Ligand information
>5r1r Chain D (length=18) Species: 562 (Escherichia coli) [Search peptide sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
VGQIDSEVDTDDLSNFQL
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5r1r A new mechanism-based radical intermediate in a mutant R1 protein affecting the catalytically essential Glu441 in Escherichia coli ribonucleotide reductase.
Resolution3.1 Å
Binding residue
(original residue number in PDB)		K341 L348 K584 K708 V709 M711 Q712 L719 K723
Binding residue
(residue number reindexed from 1)		K341 L348 K584 K708 V709 M711 Q712 L719 K723
Enzymatic activity
Catalytic site (original residue number in PDB) C225 N437 C439 A441 C462 Y730 Y731
Catalytic site (residue number reindexed from 1) C225 N437 C439 A441 C462 Y730 Y731
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:0005515 protein binding
GO:0005524 ATP binding
GO:0016491 oxidoreductase activity
GO:0042802 identical protein binding
GO:0044183 protein folding chaperone
Biological Process
GO:0006457 protein folding
GO:0009185 ribonucleoside diphosphate metabolic process
GO:0009263 deoxyribonucleotide biosynthetic process
GO:0009265 2'-deoxyribonucleotide biosynthetic process
GO:0015949 nucleobase-containing small molecule interconversion
Cellular Component
GO:0005829 cytosol
GO:0005971 ribonucleoside-diphosphate reductase complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:5r1r, PDBe:5r1r, PDBj:5r1r
PDBsum5r1r
PubMed9395490
UniProtP00452|RIR1_ECOLI Ribonucleoside-diphosphate reductase 1 subunit alpha (Gene Name=nrdA)

[Back to BioLiP]