PDB entry 3b9x

View 3b9x on RCSB PDB site
Description: Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine
Class: hydrolase
Keywords: Open (alpha, beta) structure, NH-fold, enzyme-substrate complex, protein-nucleoside complex, Glycosidase, Hydrolase, Metal-binding
Deposited on 2007-11-07, released 2008-04-01
The last revision prior to the SCOPe 2.01 freeze date was dated 2011-07-13, with a file datestamp of 2011-05-08.
Experiment type: XRAY
Resolution: 2.3 Å
R-factor: 0.203
AEROSPACI score: 0.35 (click here for full SPACI score report)

Chains and heterogens:

  • Chain 'A':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihB
    Species: Escherichia coli [TaxId:83333]
    Gene: rihB, yeiK
    Database cross-references and differences (RAF-indexed):
    • Uniprot P33022
      • see remark 999 (103)
    Domains in SCOPe 2.01: d3b9xa1
  • Chain 'B':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihB
    Species: Escherichia coli [TaxId:83333]
    Gene: rihB, yeiK
    Database cross-references and differences (RAF-indexed):
    • Uniprot P33022
      • see remark 999 (103)
    Domains in SCOPe 2.01: d3b9xb1
  • Chain 'C':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihB
    Species: Escherichia coli [TaxId:83333]
    Gene: rihB, yeiK
    Database cross-references and differences (RAF-indexed): Domains in SCOPe 2.01: d3b9xc1
  • Chain 'D':
    Compound: Pyrimidine-specific ribonucleoside hydrolase rihB
    Species: Escherichia coli [TaxId:83333]
    Gene: rihB, yeiK
    Database cross-references and differences (RAF-indexed):
    • Uniprot P33022
      • see remark 999 (103)
    Domains in SCOPe 2.01: d3b9xd1
  • Heterogens: CA, NOS, TAM, HOH

PDB Chain Sequences:

  • Chain 'A':
    Sequence, based on SEQRES records: (download) 
    >3b9xA (A:)
mgsshhhhhhssglvprgshmekrkiildcdpghddaiaimmaakhpaidllgitivagn
qtldktlinglnvcqkleinvpvyagmpqpimrqqivadnihgdtgldgpvfepltrqae
sthavkyiidtlmasdgditlvpvgplsniavamrmqpailpkireivlmggaygtgnft
psaefnifadpeaarvvftsgvplvmmgldltnqtvctpdviarmeraggpagelfsdim
nftlktqfenyglaggpvhdatcigylinpdgiktqemyvevdvnsgpcygrtvcdelgv
lgkpantkvgitidtdwfwglveecvrgyikth

    Sequence, based on observed residues (ATOM records): (download) 
    >3b9xA (A:)
krkiildcdpghddaiaimmaakhpaidllgitivagnqtldktlinglnvcqkleinvp
vyagmpqpimrqqivadnihgdtgldgpvfepltrqaesthavkyiidtlmasdgditlv
pvgplsniavamrmqpailpkireivlmggaygtgnftpsaefnifadpeaarvvftsgv
plvmmgldltnqtvctpdviarmeraggpagelfsdimnftlktqfenyglaggpvhdat
cigylinpdgiktqemyvevdvnsgpcygrtvcdelgvlgkpantkvgitidtdwfwglv
eecvrgyik

  • Chain 'B':
    Sequence, based on SEQRES records: (download) 
    >3b9xB (B:)
mgsshhhhhhssglvprgshmekrkiildcdpghddaiaimmaakhpaidllgitivagn
qtldktlinglnvcqkleinvpvyagmpqpimrqqivadnihgdtgldgpvfepltrqae
sthavkyiidtlmasdgditlvpvgplsniavamrmqpailpkireivlmggaygtgnft
psaefnifadpeaarvvftsgvplvmmgldltnqtvctpdviarmeraggpagelfsdim
nftlktqfenyglaggpvhdatcigylinpdgiktqemyvevdvnsgpcygrtvcdelgv
lgkpantkvgitidtdwfwglveecvrgyikth

    Sequence, based on observed residues (ATOM records): (download) 
    >3b9xB (B:)
krkiildcdpghddaiaimmaakhpaidllgitivagnqtldktlinglnvcqkleinvp
vyagmpqpimrqqivadtgldgpvfepltrqaesthavkyiidtlmasdgditlvpvgpl
sniavamrmqpailpkireivlmggaygtgnftpsaefnifadpeaarvvftsgvplvmm
gldltnqtvctpdviarmeraggpagelfsdimnftlktqfenyglaggpvhdatcigyl
inpdgiktqemyvevdvnsgpcygrtvcdelgvlgkpantkvgitidtdwfwglveecvr
gyi

  • Chain 'C':
    Sequence, based on SEQRES records: (download) 
    >3b9xC (C:)
mgsshhhhhhssglvprgshmekrkiildcdpghddaiaimmaakhpaidllgitivagn
qtldktlinglnvcqkleinvpvyagmpqpimrqqivadnihgdtgldgpvfepltrqae
sthavkyiidtlmasdgditlvpvgplsniavamrmqpailpkireivlmggaygtgnft
psaefnifadpeaarvvftsgvplvmmgldltnqtvctpdviarmeraggpagelfsdim
nftlktqfenyglaggpvhdatcigylinpdgiktqemyvevdvnsgpcygrtvcdelgv
lgkpantkvgitidtdwfwglveecvrgyikth

    Sequence, based on observed residues (ATOM records): (download) 
    >3b9xC (C:)
krkiildcdpghddaiaimmaakhpaidllgitivagnqtldktlinglnvcqkleinvp
vyagmpqpimrqqivatgldgpvfepltrqaesthavkyiidtlmasdgditlvpvgpls
niavamrmqpailpkireivlmggaygtgnftpsaefnifadpeaarvvftsgvplvmmg
ldltnqtvctpdviarmeraggpagelfsdpvhdatcigylinpdgiktqemyvevdvns
gpcygrtvcdelgvlgkpantkvgitidtdwfwglveecvrgy

  • Chain 'D':
    Sequence, based on SEQRES records: (download) 
    >3b9xD (D:)
mgsshhhhhhssglvprgshmekrkiildcdpghddaiaimmaakhpaidllgitivagn
qtldktlinglnvcqkleinvpvyagmpqpimrqqivadnihgdtgldgpvfepltrqae
sthavkyiidtlmasdgditlvpvgplsniavamrmqpailpkireivlmggaygtgnft
psaefnifadpeaarvvftsgvplvmmgldltnqtvctpdviarmeraggpagelfsdim
nftlktqfenyglaggpvhdatcigylinpdgiktqemyvevdvnsgpcygrtvcdelgv
lgkpantkvgitidtdwfwglveecvrgyikth

    Sequence, based on observed residues (ATOM records): (download) 
    >3b9xD (D:)
krkiildcdpghddaiaimmaakhpaidllgitivagnqtldktlinglnvcqkleinvp
vyagmpqpimrqqivaihgdtgldgpvfepltrqaesthavkyiidtlmasdgditlvpv
gplsniavamrmqpailpkireivlmggaygtgnftpsaefnifadpeaarvvftsgvpl
vmmgldltnqtvctpdviarmeraggpagelfsdimnftlktqfenyglaggpvhdatci
gylinpdgiktqemyvevdvnsgpcygrtvcdelgvlgkpantkvgitidtdwfwglvee
cvrgyik