PDB entry 3g5i

View 3g5i on RCSB PDB site
Description: Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor
Class: hydrolase
Keywords: Open (alpha, beta) structure, Glycosidase, Hydrolase
Deposited on 2009-02-05, released 2010-02-09
The last revision prior to the SCOPe 2.08 freeze date was dated 2021-02-17, with a file datestamp of 2021-02-12.
Experiment type: XRAY
Resolution: 2.1 Å
R-factor: N/A
AEROSPACI score: 0.37 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihA
    Species: Escherichia coli [TaxId:83333]
    Gene: ybeK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3g5ia_
  • Chain 'B':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihA
    Species: Escherichia coli [TaxId:83333]
    Gene: ybeK
    Database cross-references and differences (RAF-indexed):
    • Uniprot P41409 (2-311)
      • expression tag (1)
    Domains in SCOPe 2.08: d3g5ib1, d3g5ib2
  • Chain 'C':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihA
    Species: Escherichia coli [TaxId:83333]
    Gene: ybeK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.08: d3g5ic_
  • Chain 'D':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihA
    Species: Escherichia coli [TaxId:83333]
    Gene: ybeK
    Database cross-references and differences (RAF-indexed):
    • Uniprot P41409 (2-311)
      • expression tag (0-1)
    Domains in SCOPe 2.08: d3g5id1, d3g5id2
  • Heterogens: BME, CA, DNB, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3g5iA (A:)
gsalpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrt
dipvaggavkplmreliiadnvhgesgldgpalpeptfapqnctavelmaktlresaepv
tivstgpqtnvalllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfq
sgipvvmagldvthkaqihvedterfraignpvstivaelldffleyhkdekwgfvgapl
hdpctiawllkpelftsverwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgf
vdlladrlkfya

    Sequence, based on observed residues (ATOM records): (download) 
    >3g5iA (A:)
alpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrtdi
pvaggavkplmreliiadnvhgesgldgpalpeptfapqnctavelmaktlresaepvti
vstgpqtnvalllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfqsg
ipvvmagldvthkaqihvedterfraignpvstivaelldfflekwgfvgaplhdpctia
wllkpelftsverwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgfvdlladr
lkfya

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3g5iB (B:)
gsalpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrt
dipvaggavkplmreliiadnvhgesgldgpalpeptfapqnctavelmaktlresaepv
tivstgpqtnvalllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfq
sgipvvmagldvthkaqihvedterfraignpvstivaelldffleyhkdekwgfvgapl
hdpctiawllkpelftsverwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgf
vdlladrlkfya

    Sequence, based on observed residues (ATOM records): (download) 
    >3g5iB (B:)
salpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrtd
ipvaggavkplmrelgldgpalpeptfapqnctavelmaktlresaepvtivstgpqtnv
alllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfqsgipvvmagld
vthkaqihvedterfraignpvstivaelldfflkwgfvgaplhdpctiawllkpelfts
verwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgfvdlladrlkfya

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3g5iC (C:)
gsalpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrt
dipvaggavkplmreliiadnvhgesgldgpalpeptfapqnctavelmaktlresaepv
tivstgpqtnvalllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfq
sgipvvmagldvthkaqihvedterfraignpvstivaelldffleyhkdekwgfvgapl
hdpctiawllkpelftsverwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgf
vdlladrlkfya

    Sequence, based on observed residues (ATOM records): (download) 
    >3g5iC (C:)
alpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrtdi
pvaggavkplmrelgldgpalpeptfapqnctavelmaktlresaepvtivstgpqtnva
lllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfqsgipvvmagldv
thkaqihvedterfraignpvstivaelldfekwgfvgaplhdpctiawllkpelftsve
rwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgfvdlladrlkfya

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3g5iD (D:)
gsalpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrt
dipvaggavkplmreliiadnvhgesgldgpalpeptfapqnctavelmaktlresaepv
tivstgpqtnvalllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfq
sgipvvmagldvthkaqihvedterfraignpvstivaelldffleyhkdekwgfvgapl
hdpctiawllkpelftsverwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgf
vdlladrlkfya

    Sequence, based on observed residues (ATOM records): (download) 
    >3g5iD (D:)
gsalpilldcdpghddaiaivlalaspeldvkaitssagnqtpektlrnvlrmltllnrt
dipvaggavkplmrelisgldgpalpeptfapqnctavelmaktlresaepvtivstgpq
tnvalllnshpelhskiarivimggamglgnwtpaaefniyvdpeaaeivfqsgipvvma
gldvthkaqihvedterfraignpvstivaelldffleyhkdekwgfvgaplhdpctiaw
llkpelftsverwvgvetqgkytqgmtvvdyyyltgnkpnatvmvdvdrqgfvdlladrl
kfya