Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

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	Active site: {"description":"Nucleophile or proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_01936","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25010423","evidenceCode":"ECO:0000303"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	72
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01936","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25010423","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)