4K4B
X-ray crystal structure of E. coli YdiI complexed with undeca-2-one-CoA
Functional Information from GO Data
Chain | GOid | namespace | contents |
A | 0005829 | cellular_component | cytosol |
A | 0009234 | biological_process | menaquinone biosynthetic process |
A | 0016289 | molecular_function | acyl-CoA hydrolase activity |
A | 0016787 | molecular_function | hydrolase activity |
A | 0016790 | molecular_function | thiolester hydrolase activity |
A | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
B | 0005829 | cellular_component | cytosol |
B | 0009234 | biological_process | menaquinone biosynthetic process |
B | 0016289 | molecular_function | acyl-CoA hydrolase activity |
B | 0016787 | molecular_function | hydrolase activity |
B | 0016790 | molecular_function | thiolester hydrolase activity |
B | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
C | 0005829 | cellular_component | cytosol |
C | 0009234 | biological_process | menaquinone biosynthetic process |
C | 0016289 | molecular_function | acyl-CoA hydrolase activity |
C | 0016787 | molecular_function | hydrolase activity |
C | 0016790 | molecular_function | thiolester hydrolase activity |
C | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
D | 0005829 | cellular_component | cytosol |
D | 0009234 | biological_process | menaquinone biosynthetic process |
D | 0016289 | molecular_function | acyl-CoA hydrolase activity |
D | 0016787 | molecular_function | hydrolase activity |
D | 0016790 | molecular_function | thiolester hydrolase activity |
D | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
E | 0005829 | cellular_component | cytosol |
E | 0009234 | biological_process | menaquinone biosynthetic process |
E | 0016289 | molecular_function | acyl-CoA hydrolase activity |
E | 0016787 | molecular_function | hydrolase activity |
E | 0016790 | molecular_function | thiolester hydrolase activity |
E | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
F | 0005829 | cellular_component | cytosol |
F | 0009234 | biological_process | menaquinone biosynthetic process |
F | 0016289 | molecular_function | acyl-CoA hydrolase activity |
F | 0016787 | molecular_function | hydrolase activity |
F | 0016790 | molecular_function | thiolester hydrolase activity |
F | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
G | 0005829 | cellular_component | cytosol |
G | 0009234 | biological_process | menaquinone biosynthetic process |
G | 0016289 | molecular_function | acyl-CoA hydrolase activity |
G | 0016787 | molecular_function | hydrolase activity |
G | 0016790 | molecular_function | thiolester hydrolase activity |
G | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
H | 0005829 | cellular_component | cytosol |
H | 0009234 | biological_process | menaquinone biosynthetic process |
H | 0016289 | molecular_function | acyl-CoA hydrolase activity |
H | 0016787 | molecular_function | hydrolase activity |
H | 0016790 | molecular_function | thiolester hydrolase activity |
H | 0061522 | molecular_function | 1,4-dihydroxy-2-naphthoyl-CoA thioesterase activity |
Functional Information from PDB Data
site_id | AC1 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE UOQ A 201 |
Chain | Residue |
A | VAL42 |
A | HOH390 |
A | HOH403 |
A | HOH411 |
A | HOH416 |
B | ALA14 |
B | MET15 |
B | GLU17 |
B | GLY18 |
B | ASN19 |
E | PHE50 |
A | ASP43 |
E | UOQ204 |
F | ILE7 |
F | MET15 |
F | TYR71 |
F | LYS79 |
F | VAL80 |
A | SER44 |
A | LYS47 |
A | GLN48 |
A | PRO49 |
A | ARG94 |
A | GLU95 |
A | HOH331 |
site_id | AC2 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL A 202 |
Chain | Residue |
A | TYR71 |
A | VAL80 |
D | UOQ501 |
site_id | AC3 |
Number of Residues | 28 |
Details | BINDING SITE FOR RESIDUE UOQ A 203 |
Chain | Residue |
A | GLN48 |
A | PRO49 |
A | HIS54 |
A | GLY55 |
A | HIS89 |
A | VAL90 |
A | ARG91 |
A | ARG94 |
A | HOH399 |
A | HOH421 |
B | LEU12 |
B | MET15 |
B | GLY16 |
B | VAL21 |
B | PHE28 |
B | GLU63 |
B | SER67 |
B | VAL81 |
B | GLY82 |
B | LEU83 |
B | LEU136 |
B | HOH343 |
B | HOH405 |
C | HIS106 |
C | GLY108 |
C | SER109 |
C | ARG110 |
C | HIS111 |
site_id | AC4 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE UOQ B 201 |
Chain | Residue |
B | HIS106 |
B | GLY108 |
B | SER109 |
B | ARG110 |
B | HIS111 |
B | HOH359 |
B | HOH379 |
C | LEU12 |
C | MET15 |
C | PHE28 |
C | GLU63 |
C | SER67 |
C | VAL68 |
C | VAL81 |
C | GLY82 |
C | LEU83 |
D | PRO49 |
D | LEU53 |
D | HIS54 |
D | GLY55 |
D | HIS89 |
D | VAL90 |
D | ARG91 |
D | SER92 |
site_id | AC5 |
Number of Residues | 24 |
Details | BINDING SITE FOR RESIDUE UOQ B 202 |
Chain | Residue |
D | GLY108 |
D | SER109 |
D | ARG110 |
D | HIS111 |
D | UOQ501 |
A | LEU12 |
A | GLY16 |
A | GLU63 |
A | SER67 |
A | VAL81 |
A | GLY82 |
A | LEU83 |
A | LEU136 |
B | GLN48 |
B | PRO49 |
B | HIS54 |
B | GLY55 |
B | HIS89 |
B | VAL90 |
B | ARG91 |
B | HOH304 |
B | HOH391 |
B | HOH411 |
D | HIS106 |
site_id | AC6 |
Number of Residues | 21 |
Details | BINDING SITE FOR RESIDUE UOQ C 201 |
Chain | Residue |
A | HIS106 |
A | GLY108 |
A | SER109 |
A | ARG110 |
A | HIS111 |
C | GLN48 |
C | PRO49 |
C | HIS54 |
C | GLY55 |
C | HIS89 |
C | VAL90 |
C | ARG91 |
C | HOH342 |
D | LEU12 |
D | GLU63 |
D | SER67 |
D | VAL68 |
D | VAL81 |
D | GLY82 |
D | HOH693 |
H | UOQ201 |
site_id | AC7 |
Number of Residues | 22 |
Details | BINDING SITE FOR RESIDUE UOQ D 501 |
Chain | Residue |
A | VAL68 |
A | TYR71 |
A | LYS79 |
A | VAL80 |
A | CL202 |
B | PHE50 |
B | UOQ202 |
B | HOH318 |
B | HOH354 |
B | HOH377 |
C | ALA14 |
C | MET15 |
C | GLY18 |
C | ASN19 |
C | HOH306 |
D | LYS47 |
D | PRO49 |
D | HOH644 |
D | HOH656 |
D | HOH685 |
D | HOH695 |
D | HOH697 |
site_id | AC8 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE UOQ E 201 |
Chain | Residue |
A | PHE50 |
A | ARG94 |
B | ILE7 |
B | MET15 |
B | TYR71 |
B | LYS79 |
B | VAL80 |
B | HOH402 |
E | VAL42 |
E | ASP43 |
E | SER44 |
E | LYS47 |
E | GLN48 |
E | PRO49 |
E | GLU95 |
E | GLY96 |
E | HOH722 |
E | HOH726 |
E | HOH757 |
E | HOH766 |
E | HOH776 |
F | ALA11 |
F | MET15 |
F | GLU17 |
F | GLY18 |
F | ASN19 |
site_id | AC9 |
Number of Residues | 3 |
Details | BINDING SITE FOR RESIDUE CL E 202 |
Chain | Residue |
E | TYR71 |
E | VAL80 |
H | UOQ202 |
site_id | BC1 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE UOQ E 203 |
Chain | Residue |
E | HIS106 |
E | GLY108 |
E | SER109 |
E | ARG110 |
E | HIS111 |
E | HOH763 |
E | HOH770 |
E | HOH786 |
G | PRO49 |
G | HIS54 |
G | GLY55 |
G | HIS89 |
G | VAL90 |
G | ARG91 |
G | HOH248 |
H | LEU12 |
H | MET15 |
H | PHE28 |
H | GLU63 |
H | SER67 |
H | VAL68 |
H | VAL81 |
H | GLY82 |
site_id | BC2 |
Number of Residues | 25 |
Details | BINDING SITE FOR RESIDUE UOQ E 204 |
Chain | Residue |
A | UOQ201 |
E | GLN48 |
E | PRO49 |
E | HIS54 |
E | GLY55 |
E | HIS89 |
E | VAL90 |
E | ARG91 |
E | HOH774 |
E | HOH781 |
F | LEU12 |
F | MET15 |
F | PHE28 |
F | GLU63 |
F | SER67 |
F | VAL81 |
F | GLY82 |
F | LEU83 |
F | LEU136 |
F | HOH370 |
G | HIS106 |
G | GLY108 |
G | SER109 |
G | ARG110 |
G | HIS111 |
site_id | BC3 |
Number of Residues | 19 |
Details | BINDING SITE FOR RESIDUE UOQ F 201 |
Chain | Residue |
F | HIS106 |
F | GLY108 |
F | SER109 |
F | ARG110 |
F | HIS111 |
F | HOH378 |
G | MET15 |
G | GLU63 |
G | VAL81 |
G | GLY82 |
G | LEU83 |
H | GLN48 |
H | PRO49 |
H | LEU53 |
H | HIS54 |
H | GLY55 |
H | HIS89 |
H | VAL90 |
H | ARG91 |
site_id | BC4 |
Number of Residues | 20 |
Details | BINDING SITE FOR RESIDUE UOQ H 201 |
Chain | Residue |
C | PHE50 |
C | UOQ201 |
D | ILE7 |
D | MET15 |
D | TYR71 |
D | LEU72 |
D | LYS79 |
D | VAL80 |
G | ASP43 |
G | SER44 |
G | LYS47 |
G | PRO49 |
G | HOH221 |
H | ALA14 |
H | MET15 |
H | GLU17 |
H | GLY18 |
H | ASN19 |
H | HOH305 |
H | HOH306 |
site_id | BC5 |
Number of Residues | 23 |
Details | BINDING SITE FOR RESIDUE UOQ H 202 |
Chain | Residue |
E | ARG5 |
E | LYS6 |
E | ILE7 |
E | LEU12 |
E | MET15 |
E | TYR71 |
E | LYS79 |
E | CL202 |
F | PHE50 |
F | HOH335 |
G | ALA11 |
G | ALA14 |
G | MET15 |
G | GLU17 |
G | GLY18 |
G | ASN19 |
H | ASP43 |
H | SER44 |
H | LYS47 |
H | PRO49 |
H | UOQ203 |
H | HOH385 |
H | HOH428 |
site_id | BC6 |
Number of Residues | 26 |
Details | BINDING SITE FOR RESIDUE UOQ H 203 |
Chain | Residue |
E | LEU12 |
E | GLU63 |
E | SER67 |
E | VAL68 |
E | VAL81 |
E | GLY82 |
E | LEU83 |
E | LEU136 |
F | GLN48 |
F | PRO49 |
F | HIS54 |
F | GLY55 |
F | HIS89 |
F | VAL90 |
F | ARG91 |
F | HOH344 |
H | HIS106 |
H | GLY108 |
H | SER109 |
H | ARG110 |
H | HIS111 |
H | UOQ202 |
H | HOH301 |
H | HOH372 |
H | HOH424 |
H | HOH427 |
Functional Information from SwissProt/UniProt
site_id | SWS_FT_FI1 |
Number of Residues | 8 |
Details | ACT_SITE: Nucleophile or proton acceptor => ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000303|PubMed:25010423 |
Chain | Residue | Details |
A | GLU63 | |
B | GLU63 | |
C | GLU63 | |
D | GLU63 | |
E | GLU63 | |
F | GLU63 | |
G | GLU63 | |
H | GLU63 |
site_id | SWS_FT_FI2 |
Number of Residues | 24 |
Details | BINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01936, ECO:0000269|PubMed:25010423 |
Chain | Residue | Details |
A | GLY82 | |
D | GLY82 | |
D | HIS89 | |
D | HIS106 | |
E | GLY82 | |
E | HIS89 | |
E | HIS106 | |
F | GLY82 | |
F | HIS89 | |
F | HIS106 | |
G | GLY82 | |
A | HIS89 | |
G | HIS89 | |
G | HIS106 | |
H | GLY82 | |
H | HIS89 | |
H | HIS106 | |
A | HIS106 | |
B | GLY82 | |
B | HIS89 | |
B | HIS106 | |
C | GLY82 | |
C | HIS89 | |
C | HIS106 |