1Q8F
Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005509 | molecular_function | calcium ion binding |
A | 0005829 | cellular_component | cytosol |
A | 0006139 | biological_process | nucleobase-containing compound metabolic process |
A | 0006152 | biological_process | purine nucleoside catabolic process |
A | 0006206 | biological_process | pyrimidine nucleobase metabolic process |
A | 0008477 | molecular_function | purine nucleosidase activity |
A | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
A | 0016799 | molecular_function | hydrolase activity, hydrolyzing N-glycosyl compounds |
A | 0032991 | cellular_component | protein-containing complex |
A | 0042802 | molecular_function | identical protein binding |
A | 0045437 | molecular_function | uridine nucleosidase activity |
A | 0046133 | biological_process | pyrimidine ribonucleoside catabolic process |
A | 0046872 | molecular_function | metal ion binding |
A | 0050263 | molecular_function | ribosylpyrimidine nucleosidase activity |
A | 0051289 | biological_process | protein homotetramerization |
B | 0005509 | molecular_function | calcium ion binding |
B | 0005829 | cellular_component | cytosol |
B | 0006139 | biological_process | nucleobase-containing compound metabolic process |
B | 0006152 | biological_process | purine nucleoside catabolic process |
B | 0006206 | biological_process | pyrimidine nucleobase metabolic process |
B | 0008477 | molecular_function | purine nucleosidase activity |
B | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
B | 0016799 | molecular_function | hydrolase activity, hydrolyzing N-glycosyl compounds |
B | 0032991 | cellular_component | protein-containing complex |
B | 0042802 | molecular_function | identical protein binding |
B | 0045437 | molecular_function | uridine nucleosidase activity |
B | 0046133 | biological_process | pyrimidine ribonucleoside catabolic process |
B | 0046872 | molecular_function | metal ion binding |
B | 0050263 | molecular_function | ribosylpyrimidine nucleosidase activity |
B | 0051289 | biological_process | protein homotetramerization |
C | 0005509 | molecular_function | calcium ion binding |
C | 0005829 | cellular_component | cytosol |
C | 0006139 | biological_process | nucleobase-containing compound metabolic process |
C | 0006152 | biological_process | purine nucleoside catabolic process |
C | 0006206 | biological_process | pyrimidine nucleobase metabolic process |
C | 0008477 | molecular_function | purine nucleosidase activity |
C | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
C | 0016799 | molecular_function | hydrolase activity, hydrolyzing N-glycosyl compounds |
C | 0032991 | cellular_component | protein-containing complex |
C | 0042802 | molecular_function | identical protein binding |
C | 0045437 | molecular_function | uridine nucleosidase activity |
C | 0046133 | biological_process | pyrimidine ribonucleoside catabolic process |
C | 0046872 | molecular_function | metal ion binding |
C | 0050263 | molecular_function | ribosylpyrimidine nucleosidase activity |
C | 0051289 | biological_process | protein homotetramerization |
D | 0005509 | molecular_function | calcium ion binding |
D | 0005829 | cellular_component | cytosol |
D | 0006139 | biological_process | nucleobase-containing compound metabolic process |
D | 0006152 | biological_process | purine nucleoside catabolic process |
D | 0006206 | biological_process | pyrimidine nucleobase metabolic process |
D | 0008477 | molecular_function | purine nucleosidase activity |
D | 0016798 | molecular_function | hydrolase activity, acting on glycosyl bonds |
D | 0016799 | molecular_function | hydrolase activity, hydrolyzing N-glycosyl compounds |
D | 0032991 | cellular_component | protein-containing complex |
D | 0042802 | molecular_function | identical protein binding |
D | 0045437 | molecular_function | uridine nucleosidase activity |
D | 0046133 | biological_process | pyrimidine ribonucleoside catabolic process |
D | 0046872 | molecular_function | metal ion binding |
D | 0050263 | molecular_function | ribosylpyrimidine nucleosidase activity |
D | 0051289 | biological_process | protein homotetramerization |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA A 2001 |
Chain | Residue |
A | ASP11 |
A | ASP16 |
A | VAL124 |
A | ASP240 |
A | GOL3001 |
A | HOH3022 |
A | HOH3026 |
site_id | AC2 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA B 2002 |
Chain | Residue |
B | VAL124 |
B | ASP240 |
B | GOL3002 |
B | HOH3028 |
B | HOH3041 |
B | ASP11 |
B | ASP16 |
site_id | AC3 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA C 2003 |
Chain | Residue |
C | ASP11 |
C | ASP16 |
C | VAL124 |
C | ASP240 |
C | GOL3003 |
C | HOH3027 |
C | HOH3047 |
site_id | AC4 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE CA D 2004 |
Chain | Residue |
D | ASP11 |
D | ASP16 |
D | VAL124 |
D | ASP240 |
D | GOL3004 |
D | HOH3023 |
D | HOH3039 |
site_id | AC5 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE GOL A 3001 |
Chain | Residue |
A | ASP15 |
A | VAL124 |
A | MET150 |
A | ASN158 |
A | GLU164 |
A | PHE165 |
A | ASN166 |
A | ASP240 |
A | CA2001 |
A | GOL3005 |
A | HOH3022 |
A | HOH3026 |
site_id | AC6 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE GOL B 3002 |
Chain | Residue |
B | ASP15 |
B | VAL124 |
B | MET150 |
B | ASN158 |
B | GLU164 |
B | PHE165 |
B | ASN166 |
B | HIS239 |
B | ASP240 |
B | CA2002 |
B | GOL3006 |
B | HOH3028 |
B | HOH3041 |
site_id | AC7 |
Number of Residues | 13 |
Details | BINDING SITE FOR RESIDUE GOL C 3003 |
Chain | Residue |
C | ASP15 |
C | VAL124 |
C | MET150 |
C | ASN158 |
C | GLU164 |
C | PHE165 |
C | ASN166 |
C | ASP240 |
C | CA2003 |
C | GOL3007 |
C | HOH3027 |
C | HOH3047 |
C | HOH3071 |
site_id | AC8 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE GOL D 3004 |
Chain | Residue |
D | ASP15 |
D | VAL124 |
D | MET150 |
D | ASN158 |
D | GLU164 |
D | PHE165 |
D | ASN166 |
D | ASP240 |
D | CA2004 |
D | GOL3008 |
D | HOH3023 |
D | HOH3039 |
site_id | AC9 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL A 3005 |
Chain | Residue |
A | ASN40 |
A | ALA78 |
A | HIS82 |
A | ASN158 |
A | PHE159 |
A | PHE165 |
A | TYR231 |
A | GOL3001 |
A | HOH3095 |
site_id | BC1 |
Number of Residues | 10 |
Details | BINDING SITE FOR RESIDUE GOL B 3006 |
Chain | Residue |
B | ASN40 |
B | ALA78 |
B | HIS82 |
B | ASN158 |
B | PHE159 |
B | PHE165 |
B | TYR231 |
B | GOL3002 |
B | HOH3067 |
B | HOH3088 |
site_id | BC2 |
Number of Residues | 12 |
Details | BINDING SITE FOR RESIDUE GOL C 3007 |
Chain | Residue |
C | ILE81 |
C | HIS82 |
C | ASN158 |
C | PHE159 |
C | PHE165 |
C | TYR231 |
C | GOL3003 |
C | HOH3071 |
C | HOH3158 |
C | HOH3282 |
C | ASN40 |
C | ALA78 |
site_id | BC3 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL D 3008 |
Chain | Residue |
D | ASN40 |
D | ALA78 |
D | HIS82 |
D | ASN158 |
D | PHE159 |
D | PHE165 |
D | TYR231 |
D | GOL3004 |
D | HOH3108 |
site_id | BC4 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE GOL A 3009 |
Chain | Residue |
A | GLN74 |
A | GOL3015 |
A | HOH3274 |
site_id | BC5 |
Number of Residues | 5 |
Details | BINDING SITE FOR RESIDUE GOL A 3010 |
Chain | Residue |
A | ARG135 |
A | VAL176 |
A | THR179 |
A | HOH3091 |
B | GOL3011 |
site_id | BC6 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL B 3011 |
Chain | Residue |
A | ARG135 |
A | GOL3010 |
B | GLN69 |
B | PRO70 |
B | ARG73 |
B | GLN74 |
B | GLN75 |
site_id | BC7 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL C 3012 |
Chain | Residue |
C | MET134 |
C | ARG135 |
C | VAL176 |
C | THR179 |
C | SER180 |
D | GLN74 |
D | GOL3014 |
D | HOH3050 |
site_id | BC8 |
Number of Residues | 8 |
Details | BINDING SITE FOR RESIDUE GOL D 3014 |
Chain | Residue |
C | ARG135 |
C | GOL3012 |
D | GLN69 |
D | PRO70 |
D | ARG73 |
D | GLN74 |
D | GLN75 |
D | HOH3311 |
site_id | BC9 |
Number of Residues | 7 |
Details | BINDING SITE FOR RESIDUE GOL A 3015 |
Chain | Residue |
A | GLN69 |
A | PRO70 |
A | ARG73 |
A | GLN74 |
A | GLN75 |
A | GOL3009 |
B | ARG135 |
site_id | CC1 |
Number of Residues | 9 |
Details | BINDING SITE FOR RESIDUE GOL C 3016 |
Chain | Residue |
C | GLN69 |
C | PRO70 |
C | ARG73 |
C | GLN74 |
C | GLN75 |
C | HOH3298 |
D | ARG135 |
D | GOL3017 |
D | HOH3239 |
site_id | CC2 |
Number of Residues | 6 |
Details | BINDING SITE FOR RESIDUE GOL D 3017 |
Chain | Residue |
C | GOL3016 |
D | ARG135 |
D | VAL176 |
D | THR179 |
D | HOH3040 |
D | HOH3109 |
Functional Information from PROSITE/UniProt
site_id | PS01247 |
Number of Residues | 11 |
Details | IUNH Inosine-uridine preferring nucleoside hydrolase family signature. DcDPGhDDAIA |
Chain | Residue | Details |
A | ASP9-ALA19 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 4 |
Details | ACT_SITE: Proton acceptor => ECO:0000255 |
Chain | Residue | Details |
A | ASP11 | |
B | ASP11 | |
C | ASP11 | |
D | ASP11 |
site_id | SWS_FT_FI2 |
Number of Residues | 16 |
Details | BINDING: |
Chain | Residue | Details |
A | ASP11 | |
A | ASP16 | |
D | ASP11 | |
D | ASP16 | |
D | VAL124 | |
D | ASP240 | |
A | VAL124 | |
A | ASP240 | |
B | ASP11 | |
B | ASP16 | |
B | VAL124 | |
B | ASP240 | |
C | ASP11 | |
C | ASP16 | |
C | VAL124 | |
C | ASP240 |
site_id | SWS_FT_FI3 |
Number of Residues | 8 |
Details | BINDING: BINDING => ECO:0000250 |
Chain | Residue | Details |
C | GLN227 | |
C | HIS239 | |
D | GLN227 | |
D | HIS239 | |
A | GLN227 | |
A | HIS239 | |
B | GLN227 | |
B | HIS239 |