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CRYSTAL STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE FROM THERMUS THERMOPHILUS HB8 IN COMPLEX WITH ATP AND ADP

TITLE

NUCLEOTIDE DIPHOSPHATE KINASE

COMPND

PHS C 138
7	A	MET
9	A	LYS
48	A	HIS
49	A	TYR
115	A	HIS
PHS I 138
7	G	MET
9	G	LYS
48	G	HIS
49	G	TYR
115	G	HIS
PHS U 138
7	S	MET
9	S	LYS

PHS G 138
48	S	HIS
49	S	TYR
115	S	HIS
7	E	MET
9	E	LYS
48	E	HIS
49	E	TYR
115	E	HIS
PHS O 138
7	M	MET
9	M	LYS
48	M	HIS
49	M	TYR
115	M	HIS

PHS A 138
7	Y	MET
9	Y	LYS
48	Y	HIS
49	Y	TYR
115	Y	HIS
ADP B 646
9	A	LYS
49	A	TYR
51	A	GLU
52	A	HIS
57	A	PHE
61	A	LEU
64	A	PHE
85	A	ARG

ADP H 646
91	A	THR
92	A	HIS
102	A	ARG
109	A	ILE
110	A	ASP
112	A	ASN
115	A	HIS
116	A	GLY
118	A	ALA
9	G	LYS
49	G	TYR
51	G	GLU
52	G	HIS
57	G	PHE

ATP W 856
61	G	LEU
85	G	ARG
91	G	THR
92	G	HIS
102	G	ARG
109	G	ILE
110	G	ASP
112	G	ASN
115	G	HIS
116	G	GLY
118	G	ALA
9	V	LYS
48	V	HIS
49	V	TYR

52	V	HIS
55	J	LYS
56	J	PRO
57	V	PHE
60	V	GLY
61	V	LEU
64	V	PHE
85	V	ARG
91	V	THR
92	J	HIS
94	J	LYS
102	V	ARG
109	V	ILE
110	V	ASP
112	V	ASN

ADP T 646
115	V	HIS
118	V	ALA
9	S	LYS
49	S	TYR
51	S	GLU
52	S	HIS
57	S	PHE
61	S	LEU
85	S	ARG
91	S	THR
92	S	HIS
102	S	ARG
109	S	ILE
110	S	ASP

ADP F 646
112	S	ASN
115	S	HIS
118	S	ALA
9	E	LYS
49	E	TYR
51	E	GLU
52	E	HIS
57	E	PHE
61	E	LEU
64	E	PHE
85	E	ARG
91	E	THR
92	E	HIS
102	E	ARG

ATP Q 856
109	E	ILE
110	E	ASP
112	E	ASN
115	E	HIS
116	E	GLY
118	E	ALA
9	P	LYS
48	P	HIS
49	P	TYR
52	P	HIS
55	H	LYS
56	H	PRO
57	P	PHE
60	P	GLY

ADP N 646
61	P	LEU
64	P	PHE
85	P	ARG
91	P	THR
92	H	HIS
94	H	LYS
102	P	ARG
109	P	ILE
110	P	ASP
112	P	ASN
115	P	HIS
118	P	ALA
9	M	LYS
49	M	TYR

51	M	GLU
52	M	HIS
57	M	PHE
61	M	LEU
64	M	PHE
85	M	ARG
91	M	THR
92	M	HIS
102	M	ARG
109	M	ILE
110	M	ASP
112	M	ASN
115	M	HIS
116	M	GLY
118	M	ALA

ADP Z 646
9	Y	LYS
49	Y	TYR
51	Y	GLU
52	Y	HIS
57	Y	PHE
61	Y	LEU
64	Y	PHE
85	Y	ARG
91	Y	THR
92	Y	HIS
102	Y	ARG
109	Y	ILE
110	Y	ASP
112	Y	ASN

ATP C 856
115	Y	HIS
116	Y	GLY
118	Y	ALA
9	B	LYS
48	B	HIS
49	B	TYR
52	B	HIS
55	D	LYS
56	D	PRO
57	B	PHE
60	B	GLY
61	B	LEU
64	B	PHE
85	B	ARG

ATP K 856
91	B	THR
92	D	HIS
94	D	LYS
102	B	ARG
109	B	ILE
110	B	ASP
112	B	ASN
115	B	HIS
118	B	ALA
9	J	LYS
48	J	HIS
49	J	TYR
52	J	HIS
55	V	LYS

56	V	PRO
57	J	PHE
60	J	GLY
61	J	LEU
64	J	PHE
85	J	ARG
91	J	THR
92	V	HIS
94	V	LYS
102	J	ARG
109	J	ILE
110	J	ASP
112	J	ASN
115	J	HIS
118	J	ALA

ATP E 856
9	D	LYS
48	D	HIS
49	D	TYR
52	D	HIS
55	B	LYS
56	B	PRO
57	D	PHE
60	D	GLY
61	D	LEU
64	D	PHE
85	D	ARG
91	D	THR
92	B	HIS
94	B	LYS

ATP I 856
102	D	ARG
109	D	ILE
110	D	ASP
112	D	ASN
115	D	HIS
118	D	ALA
9	H	LYS
48	H	HIS
49	H	TYR
52	H	HIS
55	P	LYS
56	P	PRO
57	H	PHE
60	H	GLY

MG X 900
61	H	LEU
64	H	PHE
85	H	ARG
91	H	THR
92	P	HIS
94	P	LYS
102	H	ARG
109	H	ILE
110	H	ASP
112	H	ASN
115	H	HIS
118	H	ALA
85	V	ARG
88	V	MET

MG R 900
102	V	ARG
115	V	HIS
116	V	GLY
85	P	ARG
88	P	MET
102	P	ARG
115	P	HIS
116	P	GLY
MG D 900
85	B	ARG
88	B	MET
102	B	ARG
115	B	HIS
116	B	GLY

MG L 900
85	J	ARG
88	J	MET
102	J	ARG
115	J	HIS
116	J	GLY
MG F 900
85	D	ARG
88	D	MET
102	D	ARG
115	D	HIS
116	D	GLY
MG J 900
85	H	ARG
88	H	MET

102	H	ARG
115	H	HIS
116	H	GLY

Links to external databases:

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apo-structure
pdb ID
1wkj		Details
other holo-structures
pdb ID	Ligand Unique ID
1wkk	GDPN1001	Details
	GDPK1001
	GDPH1001
	GDPQ1001
	GDPB1001
	GDPE1001

Ligand List Help

ADP	NAME:	ADENOSINE-5'-DIPHOSPHATE
	FORMULA:	C10 H15 N5 O10 P2
	SMILES:	Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(O)=O)C(O)C3O
PHS	NAME:	PHOSPHONO GROUP
	FORMULA:	H2 O3 P1
	SMILES:	OP(O)=O
ATP	NAME:	ADENOSINE-5'-TRIPHOSPHATE
	FORMULA:	C10 H16 N5 O13 P3
	SMILES:	Nc1ncnc2[n](cnc12)C3OC(COP(O)(=O)OP(O)(=O)OP(O)(O)=O)C(O)C3O
MG	NAME:	MAGNESIUM ION
	FORMULA:	MG1
	SMILES:	[Mg++]

v9.7
April 2012 Interdisciplinary Research Institute, Computational Biology, Villeneuve d'Ascq, France
University College London, Biomolecular Structure and Modelling Unit, London, UK
Hospital for Sick Children and University of Toronto, Structural Biology and Biochemistry Program, Toronto, Canada

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