Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2VYX

Crystal structure of the T. thermophilus dodecin W38F mutant

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
B	0000166	molecular_function	nucleotide binding
C	0000166	molecular_function	nucleotide binding
D	0000166	molecular_function	nucleotide binding
E	0000166	molecular_function	nucleotide binding
F	0000166	molecular_function	nucleotide binding
G	0000166	molecular_function	nucleotide binding
H	0000166	molecular_function	nucleotide binding
I	0000166	molecular_function	nucleotide binding
J	0000166	molecular_function	nucleotide binding
K	0000166	molecular_function	nucleotide binding
L	0000166	molecular_function	nucleotide binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FMN A 1070

Chain	Residue
A	TYR5
B	GLN57
A	ASP37
A	PHE38
A	ARG65
A	FMN1072
A	HOH2023
A	HOH2036
B	ARG45
B	THR47

site_id	AC2
Number of Residues	20
Details	BINDING SITE FOR RESIDUE COA A 1071

Chain	Residue
A	ARG28
A	THR32
A	ARG34
A	HIS35
A	PHE64
A	ARG65
A	LEU66
A	GLU67
A	COA1073
A	HOH2037
A	HOH2038
A	HOH2039
H	LYS6
L	LYS6
L	VAL8
L	ARG28
L	LEU33
L	PHE64
L	LEU66
L	COA1068

site_id	AC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FMN A 1072

Chain	Residue
A	FMN1070
A	HOH2040
A	HOH2041
A	HOH2042
B	GLN57
G	LYS3
G	TYR5
G	ASP37
G	PHE38
G	ARG65
H	ARG45
H	THR47
H	GLN57

site_id	AC4
Number of Residues	18
Details	BINDING SITE FOR RESIDUE COA A 1073

Chain	Residue
A	LYS6
A	VAL8
A	LEU33
A	PHE64
A	LEU66
A	COA1071
F	GLU16
H	ARG28
H	THR32
H	LEU33
H	ARG34
H	HIS35
H	PHE64
H	ARG65
H	GLU67
L	LYS6
L	LEU66
L	COA1068

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 1074

Chain	Residue
A	LYS6
A	HOH2002
H	LYS6
L	LYS6

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE FMN B 1068

Chain	Residue
B	LYS3
B	TYR5
B	ASP37
B	PHE38
B	ARG65
B	FMN1070
B	HOH2045
C	ARG45
C	THR47
C	GLN57
F	VAL11
F	GLN57

site_id	AC7
Number of Residues	18
Details	BINDING SITE FOR RESIDUE COA B 1069

Chain	Residue
B	ARG28
B	THR32
B	LEU33
B	ARG34
B	HIS35
B	PHE64
B	ARG65
B	GLU67
B	HOH2047
B	HOH2048
B	HOH2050
F	LYS6
F	LEU66
F	COA1071
G	LYS6
G	VAL8
G	LEU66
G	COA1070

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FMN B 1070

Chain	Residue
E	TYR5
E	ASP37
E	PHE38
E	ARG65
F	ARG45
F	THR47
F	GLN57
B	FMN1068
B	HOH2051
C	VAL11
E	LYS3

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 1071

Chain	Residue
B	LYS6
F	LYS6
G	LYS6

site_id	BC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FMN C 1070

Chain	Residue
A	ARG45
A	THR47
A	GLN57
C	TYR5
C	ASP37
C	PHE38
C	ARG65
C	FMN1072
C	HOH2021
C	HOH2044
J	GLN57

site_id	BC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE COA C 1071

Chain	Residue
C	ARG28
C	THR32
C	ARG34
C	HIS35
C	PHE64
C	ARG65
C	LEU66
C	GLU67
C	HOH2045
C	HOH2046
C	HOH2047
C	HOH2048
C	HOH2049
E	LYS6
E	VAL8
E	ARG28
E	LEU33
E	LEU66
E	COA1070
J	LYS6
J	LEU66
J	COA1070

site_id	BC3
Number of Residues	14
Details	BINDING SITE FOR RESIDUE FMN C 1072

Chain	Residue
A	GLN57
C	FMN1070
C	HOH2050
C	HOH2051
C	HOH2052
J	ARG45
J	THR47
J	GLN57
L	LYS3
L	TYR5
L	ASP37
L	PHE38
L	ARG65
L	HOH2010

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL C 1073

Chain	Residue
C	LYS6
E	LYS6
J	LYS6

site_id	BC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE FMN D 1070

Chain	Residue
D	LYS3
D	TYR5
D	ASP37
D	PHE38
D	ARG65
D	FMN1072
D	HOH2026
D	HOH2048
D	HOH2049
D	HOH2050
D	HOH2051
E	ARG45
E	THR47
E	GLN57
K	GLN57

site_id	BC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE COA D 1071

Chain	Residue
D	ARG28
D	THR32
D	ARG34
D	ARG65
D	LEU66
D	GLU67
D	HOH2021
D	HOH2054
I	LYS6
I	VAL8
I	PHE64
I	LEU66
I	COA1070
K	LYS6
K	COA1070
K	HOH2018
K	HOH2032

site_id	BC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FMN D 1072

Chain	Residue
D	FMN1070
D	HOH2055
D	HOH2056
E	ARG45
E	GLN57
J	TYR5
J	ASP37
J	PHE38
J	ARG65
J	HOH2021
K	ARG45
K	THR47
K	GLN57

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL D 1073

Chain	Residue
D	LYS6
I	LYS6
K	LYS6

site_id	BC9
Number of Residues	22
Details	BINDING SITE FOR RESIDUE COA E 1070

Chain	Residue
B	HIS35
B	ARG65
B	HOH2040
C	LYS6
C	COA1071
E	ARG28
E	THR32
E	LEU33
E	ARG34
E	HIS35
E	PHE64
E	ARG65
E	GLU67
E	HOH2015
E	HOH2042
E	HOH2043
J	LYS6
J	VAL8
J	LEU33
J	PHE64
J	LEU66
J	COA1070

site_id	CC1
Number of Residues	14
Details	BINDING SITE FOR RESIDUE FMN F 1070

Chain	Residue
D	ARG45
D	THR47
D	GLN57
F	LYS3
F	TYR5
F	ASP37
F	PHE38
F	ARG65
F	FMN1072
F	HOH2021
F	HOH2024
F	HOH2042
F	HOH2044
G	GLN57

site_id	CC2
Number of Residues	20
Details	BINDING SITE FOR RESIDUE COA F 1071

Chain	Residue
B	LYS6
B	VAL8
B	ALA29
B	LEU66
B	COA1069
B	HOH2047
F	ARG28
F	THR32
F	LEU33
F	ARG34
F	HIS35
F	ARG65
F	LEU66
F	GLU67
F	HOH2013
F	HOH2023
F	HOH2046
G	LYS6
G	LEU66
G	COA1070

site_id	CC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE FMN F 1072

Chain	Residue
D	GLN57
F	FMN1070
F	HOH2047
F	HOH2048
F	HOH2049
F	HOH2050
F	HOH2052
G	ARG45
G	THR47
G	GLN57
I	TYR5
I	ASP37
I	PHE38
I	ARG65
I	HOH2022

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA F 1073

Chain	Residue
D	HOH2031
D	HOH2039
F	HOH2044

site_id	CC5
Number of Residues	23
Details	BINDING SITE FOR RESIDUE COA G 1070

Chain	Residue
B	LYS6
B	LEU66
B	COA1069
B	HOH2030
D	ARG65
F	LYS6
F	VAL8
F	LEU33
F	PHE64
F	LEU66
F	COA1071
G	ARG28
G	THR32
G	LEU33
G	ARG34
G	HIS35
G	PHE64
G	ARG65
G	LEU66
G	GLU67
G	HOH2048
G	HOH2049
G	HOH2050

site_id	CC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE FMN H 1070

Chain	Residue
C	HIS35
H	TYR5
H	ASP37
H	PHE38
H	ARG65
H	FMN1071
H	HOH2032
H	HOH2033
H	HOH2034
H	HOH2035
I	ARG45
I	THR47
I	GLN57
I	HOH2028
L	GLN57

site_id	CC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FMN H 1071

Chain	Residue
H	FMN1070
H	HOH2036
H	HOH2037
I	GLN57
K	LYS3
K	TYR5
K	ASP37
K	PHE38
K	ARG65
K	HOH2017
L	ARG45
L	THR47
L	GLN57

site_id	CC8
Number of Residues	19
Details	BINDING SITE FOR RESIDUE COA I 1070

Chain	Residue
D	LYS6
D	COA1071
D	HOH2006
I	ARG28
I	THR32
I	LEU33
I	ARG34
I	HIS35
I	PHE64
I	ARG65
I	GLU67
I	HOH2043
K	LYS6
K	VAL8
K	LEU10
K	LEU33
K	PHE64
K	LEU66
K	COA1070

site_id	CC9
Number of Residues	18
Details	BINDING SITE FOR RESIDUE COA J 1070

Chain	Residue
C	LYS6
C	VAL8
C	ALA29
C	LEU33
C	PHE64
C	LEU66
C	COA1071
E	LYS6
E	LEU66
E	COA1070
J	ARG28
J	THR32
J	LEU33
J	ARG34
J	HIS35
J	ARG65
J	GLU67
J	HOH2042

site_id	DC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE COA K 1070

Chain	Residue
D	LYS6
D	VAL8
D	ARG28
D	PHE64
D	LEU66
D	COA1071
I	LYS6
I	COA1070
K	ARG28
K	THR32
K	ARG34
K	HIS35
K	PHE64
K	ARG65
K	GLU67
K	HOH2033
K	HOH2034

site_id	DC2
Number of Residues	18
Details	BINDING SITE FOR RESIDUE COA L 1068

Chain	Residue
A	LYS6
A	LEU66
A	COA1071
A	COA1073
A	HOH2038
D	ALA51
H	LYS6
H	VAL8
H	PHE64
H	LEU66
L	ARG28
L	THR32
L	ARG34
L	HIS35
L	PHE64
L	ARG65
L	GLU67
L	HOH2027

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	60
Details	BINDING: in other chain => ECO:0000269\|Ref.4

Chain	Residue	Details
A	LYS3
B	ARG65
C	LYS3
C	ARG28
C	ASP37
C	PHE38
C	ARG65
D	LYS3
D	ARG28
D	ASP37
D	PHE38
A	ARG28
D	ARG65
E	LYS3
E	ARG28
E	ASP37
E	PHE38
E	ARG65
F	LYS3
F	ARG28
F	ASP37
F	PHE38
A	ASP37
F	ARG65
G	LYS3
G	ARG28
G	ASP37
G	PHE38
G	ARG65
H	LYS3
H	ARG28
H	ASP37
H	PHE38
A	PHE38
H	ARG65
I	LYS3
I	ARG28
I	ASP37
I	PHE38
I	ARG65
J	LYS3
J	ARG28
J	ASP37
J	PHE38
A	ARG65
J	ARG65
K	LYS3
K	ARG28
K	ASP37
K	PHE38
K	ARG65
L	LYS3
L	ARG28
L	ASP37
L	PHE38
B	LYS3
L	ARG65
B	ARG28
B	ASP37
B	PHE38

site_id	SWS_FT_FI2
Number of Residues	36
Details	BINDING: BINDING => ECO:0000269\|Ref.4

Chain	Residue	Details
A	LYS6
D	LYS6
D	ARG45
D	GLN57
E	LYS6
E	ARG45
E	GLN57
F	LYS6
F	ARG45
F	GLN57
G	LYS6
A	ARG45
G	ARG45
G	GLN57
H	LYS6
H	ARG45
H	GLN57
I	LYS6
I	ARG45
I	GLN57
J	LYS6
J	ARG45
A	GLN57
J	GLN57
K	LYS6
K	ARG45
K	GLN57
L	LYS6
L	ARG45
L	GLN57
B	LYS6
B	ARG45
B	GLN57
C	LYS6
C	ARG45
C	GLN57

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: in other chain

Chain	Residue	Details
A	THR32
J	THR32
K	THR32
L	THR32
B	THR32
C	THR32
D	THR32
E	THR32
F	THR32
G	THR32
H	THR32
I	THR32

site_id	SWS_FT_FI4
Number of Residues	12
Details	SITE: May be important for ligand binding specificity and FMN binding

Chain	Residue	Details
A	ARG65
J	ARG65
K	ARG65
L	ARG65
B	ARG65
C	ARG65
D	ARG65
E	ARG65
F	ARG65
G	ARG65
H	ARG65
I	ARG65

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