Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5V6D

Crystal structure of nucleoside diphosphate kinase from Neisseria gonorrhoeae in complex with citrate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004550	molecular_function	nucleoside diphosphate kinase activity
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0006183	biological_process	GTP biosynthetic process
A	0006228	biological_process	UTP biosynthetic process
A	0006241	biological_process	CTP biosynthetic process
A	0009117	biological_process	nucleotide metabolic process
A	0009142	biological_process	nucleoside triphosphate biosynthetic process
A	0016301	molecular_function	kinase activity
A	0046872	molecular_function	metal ion binding
B	0004550	molecular_function	nucleoside diphosphate kinase activity
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0006183	biological_process	GTP biosynthetic process
B	0006228	biological_process	UTP biosynthetic process
B	0006241	biological_process	CTP biosynthetic process
B	0009117	biological_process	nucleotide metabolic process
B	0009142	biological_process	nucleoside triphosphate biosynthetic process
B	0016301	molecular_function	kinase activity
B	0046872	molecular_function	metal ion binding
C	0004550	molecular_function	nucleoside diphosphate kinase activity
C	0005524	molecular_function	ATP binding
C	0005737	cellular_component	cytoplasm
C	0006183	biological_process	GTP biosynthetic process
C	0006228	biological_process	UTP biosynthetic process
C	0006241	biological_process	CTP biosynthetic process
C	0009117	biological_process	nucleotide metabolic process
C	0009142	biological_process	nucleoside triphosphate biosynthetic process
C	0016301	molecular_function	kinase activity
C	0046872	molecular_function	metal ion binding
D	0004550	molecular_function	nucleoside diphosphate kinase activity
D	0005524	molecular_function	ATP binding
D	0005737	cellular_component	cytoplasm
D	0006183	biological_process	GTP biosynthetic process
D	0006228	biological_process	UTP biosynthetic process
D	0006241	biological_process	CTP biosynthetic process
D	0009117	biological_process	nucleotide metabolic process
D	0009142	biological_process	nucleoside triphosphate biosynthetic process
D	0016301	molecular_function	kinase activity
D	0046872	molecular_function	metal ion binding
E	0004550	molecular_function	nucleoside diphosphate kinase activity
E	0005524	molecular_function	ATP binding
E	0005737	cellular_component	cytoplasm
E	0006183	biological_process	GTP biosynthetic process
E	0006228	biological_process	UTP biosynthetic process
E	0006241	biological_process	CTP biosynthetic process
E	0009117	biological_process	nucleotide metabolic process
E	0009142	biological_process	nucleoside triphosphate biosynthetic process
E	0016301	molecular_function	kinase activity
E	0046872	molecular_function	metal ion binding
F	0004550	molecular_function	nucleoside diphosphate kinase activity
F	0005524	molecular_function	ATP binding
F	0005737	cellular_component	cytoplasm
F	0006183	biological_process	GTP biosynthetic process
F	0006228	biological_process	UTP biosynthetic process
F	0006241	biological_process	CTP biosynthetic process
F	0009117	biological_process	nucleotide metabolic process
F	0009142	biological_process	nucleoside triphosphate biosynthetic process
F	0016301	molecular_function	kinase activity
F	0046872	molecular_function	metal ion binding
G	0004550	molecular_function	nucleoside diphosphate kinase activity
G	0005524	molecular_function	ATP binding
G	0005737	cellular_component	cytoplasm
G	0006183	biological_process	GTP biosynthetic process
G	0006228	biological_process	UTP biosynthetic process
G	0006241	biological_process	CTP biosynthetic process
G	0009117	biological_process	nucleotide metabolic process
G	0009142	biological_process	nucleoside triphosphate biosynthetic process
G	0016301	molecular_function	kinase activity
G	0046872	molecular_function	metal ion binding
H	0004550	molecular_function	nucleoside diphosphate kinase activity
H	0005524	molecular_function	ATP binding
H	0005737	cellular_component	cytoplasm
H	0006183	biological_process	GTP biosynthetic process
H	0006228	biological_process	UTP biosynthetic process
H	0006241	biological_process	CTP biosynthetic process
H	0009117	biological_process	nucleotide metabolic process
H	0009142	biological_process	nucleoside triphosphate biosynthetic process
H	0016301	molecular_function	kinase activity
H	0046872	molecular_function	metal ion binding
I	0004550	molecular_function	nucleoside diphosphate kinase activity
I	0005524	molecular_function	ATP binding
I	0005737	cellular_component	cytoplasm
I	0006183	biological_process	GTP biosynthetic process
I	0006228	biological_process	UTP biosynthetic process
I	0006241	biological_process	CTP biosynthetic process
I	0009117	biological_process	nucleotide metabolic process
I	0009142	biological_process	nucleoside triphosphate biosynthetic process
I	0016301	molecular_function	kinase activity
I	0046872	molecular_function	metal ion binding
J	0004550	molecular_function	nucleoside diphosphate kinase activity
J	0005524	molecular_function	ATP binding
J	0005737	cellular_component	cytoplasm
J	0006183	biological_process	GTP biosynthetic process
J	0006228	biological_process	UTP biosynthetic process
J	0006241	biological_process	CTP biosynthetic process
J	0009117	biological_process	nucleotide metabolic process
J	0009142	biological_process	nucleoside triphosphate biosynthetic process
J	0016301	molecular_function	kinase activity
J	0046872	molecular_function	metal ion binding
K	0004550	molecular_function	nucleoside diphosphate kinase activity
K	0005524	molecular_function	ATP binding
K	0005737	cellular_component	cytoplasm
K	0006183	biological_process	GTP biosynthetic process
K	0006228	biological_process	UTP biosynthetic process
K	0006241	biological_process	CTP biosynthetic process
K	0009117	biological_process	nucleotide metabolic process
K	0009142	biological_process	nucleoside triphosphate biosynthetic process
K	0016301	molecular_function	kinase activity
K	0046872	molecular_function	metal ion binding
L	0004550	molecular_function	nucleoside diphosphate kinase activity
L	0005524	molecular_function	ATP binding
L	0005737	cellular_component	cytoplasm
L	0006183	biological_process	GTP biosynthetic process
L	0006228	biological_process	UTP biosynthetic process
L	0006241	biological_process	CTP biosynthetic process
L	0009117	biological_process	nucleotide metabolic process
L	0009142	biological_process	nucleoside triphosphate biosynthetic process
L	0016301	molecular_function	kinase activity
L	0046872	molecular_function	metal ion binding
M	0004550	molecular_function	nucleoside diphosphate kinase activity
M	0005524	molecular_function	ATP binding
M	0005737	cellular_component	cytoplasm
M	0006183	biological_process	GTP biosynthetic process
M	0006228	biological_process	UTP biosynthetic process
M	0006241	biological_process	CTP biosynthetic process
M	0009117	biological_process	nucleotide metabolic process
M	0009142	biological_process	nucleoside triphosphate biosynthetic process
M	0016301	molecular_function	kinase activity
M	0046872	molecular_function	metal ion binding
N	0004550	molecular_function	nucleoside diphosphate kinase activity
N	0005524	molecular_function	ATP binding
N	0005737	cellular_component	cytoplasm
N	0006183	biological_process	GTP biosynthetic process
N	0006228	biological_process	UTP biosynthetic process
N	0006241	biological_process	CTP biosynthetic process
N	0009117	biological_process	nucleotide metabolic process
N	0009142	biological_process	nucleoside triphosphate biosynthetic process
N	0016301	molecular_function	kinase activity
N	0046872	molecular_function	metal ion binding
O	0004550	molecular_function	nucleoside diphosphate kinase activity
O	0005524	molecular_function	ATP binding
O	0005737	cellular_component	cytoplasm
O	0006183	biological_process	GTP biosynthetic process
O	0006228	biological_process	UTP biosynthetic process
O	0006241	biological_process	CTP biosynthetic process
O	0009117	biological_process	nucleotide metabolic process
O	0009142	biological_process	nucleoside triphosphate biosynthetic process
O	0016301	molecular_function	kinase activity
O	0046872	molecular_function	metal ion binding
P	0004550	molecular_function	nucleoside diphosphate kinase activity
P	0005524	molecular_function	ATP binding
P	0005737	cellular_component	cytoplasm
P	0006183	biological_process	GTP biosynthetic process
P	0006228	biological_process	UTP biosynthetic process
P	0006241	biological_process	CTP biosynthetic process
P	0009117	biological_process	nucleotide metabolic process
P	0009142	biological_process	nucleoside triphosphate biosynthetic process
P	0016301	molecular_function	kinase activity
P	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	binding site for residue CIT A 201

Chain	Residue
A	LYS11
A	HOH335
A	TYR51
A	PHE59
A	ARG87
A	ARG104
A	ASN114
A	HIS117
A	HOH308
A	HOH314

site_id	AC2
Number of Residues	1
Details	binding site for residue EDO A 202

Chain	Residue
A	HOH329

site_id	AC3
Number of Residues	7
Details	binding site for residue EDO A 203

Chain	Residue
A	GLY31
A	LYS33
A	HOH313
B	ASN18
C	GLU28
D	LYS17
D	ASN18

site_id	AC4
Number of Residues	12
Details	binding site for residue CIT B 201

Chain	Residue
B	LYS11
B	TYR51
B	THR93
B	ARG104
B	ASN114
B	HIS117
B	HOH303
B	HOH312
B	HOH314
B	HOH329
B	HOH331
B	HOH348

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO B 202

Chain	Residue
B	LEU127
B	TYR131
B	HOH311
B	HOH368

site_id	AC6
Number of Residues	15
Details	binding site for residue CIT C 201

Chain	Residue
C	LYS11
C	TYR51
C	ARG87
C	THR93
C	ARG104
C	ASN114
C	HIS117
C	HOH311
C	HOH322
C	HOH345
C	HOH359
C	HOH371
C	HOH373
C	HOH387
C	HOH403

site_id	AC7
Number of Residues	6
Details	binding site for residue EDO C 202

Chain	Residue
C	PHE50
C	LEU127
C	GLU128
C	HOH319
C	HOH323
C	HOH353

site_id	AC8
Number of Residues	7
Details	binding site for residue EDO C 203

Chain	Residue
A	GLU28
B	LYS17
B	ASN18
B	HOH370
C	GLY31
C	LYS33
C	HOH356

site_id	AC9
Number of Residues	13
Details	binding site for residue CIT D 201

Chain	Residue
D	LYS11
D	TYR51
D	ARG104
D	ASN114
D	HIS117
D	HOH327
D	HOH334
D	HOH338
D	HOH340
D	HOH347
D	HOH356
D	HOH366
D	HOH385

site_id	AD1
Number of Residues	5
Details	binding site for residue EDO D 202

Chain	Residue
D	LEU127
D	GLU128
D	HOH311
D	HOH320
D	HOH380

site_id	AD2
Number of Residues	13
Details	binding site for residue CIT E 201

Chain	Residue
E	LYS11
E	TYR51
E	THR93
E	ARG104
E	ASN114
E	HIS117
E	HOH311
E	HOH319
E	HOH324
E	HOH339
E	HOH340
E	HOH355
E	HOH391

site_id	AD3
Number of Residues	4
Details	binding site for residue EDO E 202

Chain	Residue
E	PHE50
E	GLU128
E	HOH344
E	HOH348

site_id	AD4
Number of Residues	16
Details	binding site for residue CIT F 201

Chain	Residue
F	ARG87
F	THR93
F	ARG104
F	ASN114
F	HIS117
F	HOH301
F	HOH325
F	HOH336
F	HOH346
F	HOH351
F	HOH352
F	HOH377
F	HOH392
F	HOH396
F	LYS11
F	TYR51

site_id	AD5
Number of Residues	4
Details	binding site for residue EDO F 202

Chain	Residue
F	PHE50
F	HOH307
F	HOH314
F	HOH371

site_id	AD6
Number of Residues	13
Details	binding site for residue CIT G 201

Chain	Residue
G	LYS11
G	TYR51
G	ARG104
G	ASN114
G	HIS117
G	HOH315
G	HOH325
G	HOH333
G	HOH334
G	HOH335
G	HOH340
G	HOH355
G	HOH369

site_id	AD7
Number of Residues	2
Details	binding site for residue EDO G 202

Chain	Residue
G	GLU128
G	HOH412

site_id	AD8
Number of Residues	8
Details	binding site for residue EDO H 201

Chain	Residue
E	ASN18
F	LYS33
G	LYS17
G	ASN18
H	GLU28
H	GLU29
H	HOH1922
H	HOH1949

site_id	AD9
Number of Residues	12
Details	binding site for residue CIT H 202

Chain	Residue
H	LYS11
H	TYR51
H	ARG104
H	ASN114
H	HIS117
H	HOH1926
H	HOH1930
H	HOH1931
H	HOH1934
H	HOH1940
H	HOH1947
H	HOH1977

site_id	AE1
Number of Residues	3
Details	binding site for residue EDO H 203

Chain	Residue
H	HOH1914
H	HOH1924
H	HOH1970

site_id	AE2
Number of Residues	7
Details	binding site for residue EDO H 204

Chain	Residue
F	GLU28
G	ASN18
H	GLY31
H	LYS33
H	HOH1903
H	HOH1918
H	HOH1938

site_id	AE3
Number of Residues	12
Details	binding site for residue CIT I 201

Chain	Residue
I	LYS11
I	TYR51
I	THR93
I	ARG104
I	ASN114
I	HIS117
I	HOH321
I	HOH332
I	HOH353
I	HOH356
I	HOH368
I	HOH398

site_id	AE4
Number of Residues	6
Details	binding site for residue EDO I 202

Chain	Residue
I	PHE50
I	LEU127
I	HOH307
I	HOH311
I	HOH338
I	HOH344

site_id	AE5
Number of Residues	13
Details	binding site for residue CIT J 201

Chain	Residue
J	LYS11
J	TYR51
J	THR93
J	ARG104
J	ASN114
J	HIS117
J	HOH318
J	HOH319
J	HOH323
J	HOH325
J	HOH330
J	HOH355
J	HOH365

site_id	AE6
Number of Residues	4
Details	binding site for residue EDO J 202

Chain	Residue
J	HOH326
J	HOH347
J	HOH380
J	HOH385

site_id	AE7
Number of Residues	11
Details	binding site for residue CIT K 201

Chain	Residue
K	LYS11
K	TYR51
K	PHE59
K	ARG104
K	ASN114
K	HIS117
K	HOH334
K	HOH344
K	HOH349
K	HOH351
K	HOH355

site_id	AE8
Number of Residues	4
Details	binding site for residue EDO K 202

Chain	Residue
K	LEU127
K	HOH311
K	HOH314
K	HOH345

site_id	AE9
Number of Residues	7
Details	binding site for residue EDO K 203

Chain	Residue
I	GLU28
J	LYS17
J	ASN18
K	GLY31
K	LYS33
K	HOH317
L	ASN18

site_id	AF1
Number of Residues	13
Details	binding site for residue CIT L 201

Chain	Residue
L	LYS11
L	TYR51
L	PHE59
L	ARG104
L	ASN114
L	HIS117
L	HOH307
L	HOH335
L	HOH341
L	HOH345
L	HOH386
L	HOH410
L	HOH411

site_id	AF2
Number of Residues	6
Details	binding site for residue EDO L 202

Chain	Residue
L	PHE50
L	TYR131
L	HOH346
L	HOH374
L	HOH399
L	HOH406

site_id	AF3
Number of Residues	11
Details	binding site for residue CIT M 201

Chain	Residue
M	LYS11
M	TYR51
M	PHE59
M	ARG104
M	ASN114
M	HIS117
M	HOH311
M	HOH319
M	HOH324
M	HOH341
M	HOH342

site_id	AF4
Number of Residues	5
Details	binding site for residue EDO M 202

Chain	Residue
M	GLU128
M	TYR131
M	HOH302
M	HOH328
M	HOH360

site_id	AF5
Number of Residues	7
Details	binding site for residue EDO M 203

Chain	Residue
M	GLY31
M	LYS33
M	HOH329
N	ASN18
O	GLU28
P	LYS17
P	ASN18

site_id	AF6
Number of Residues	13
Details	binding site for residue CIT N 201

Chain	Residue
N	LYS11
N	TYR51
N	THR93
N	ARG104
N	ASN114
N	HIS117
N	HOH316
N	HOH317
N	HOH327
N	HOH343
N	HOH366
N	HOH379
N	HOH395

site_id	AF7
Number of Residues	4
Details	binding site for residue EDO N 202

Chain	Residue
N	LEU127
N	GLU128
N	HOH344
N	HOH349

site_id	AF8
Number of Residues	8
Details	binding site for residue CIT O 201

Chain	Residue
O	LYS11
O	TYR51
O	ARG104
O	ASN114
O	HIS117
O	HOH306
O	HOH312
O	HOH333

site_id	AF9
Number of Residues	5
Details	binding site for residue EDO O 202

Chain	Residue
O	PHE50
O	ASN124
O	GLU128
O	HOH301
O	HOH331

site_id	AG1
Number of Residues	13
Details	binding site for residue CIT P 201

Chain	Residue
P	LYS11
P	TYR51
P	THR93
P	ARG104
P	ASN114
P	HIS117
P	HOH306
P	HOH324
P	HOH326
P	HOH330
P	HOH336
P	HOH339
P	HOH340

site_id	AG2
Number of Residues	3
Details	binding site for residue EDO P 202

Chain	Residue
P	LEU127
P	HOH342
P	HOH355

Functional Information from PROSITE/UniProt

site_id	PS00469
Number of Residues	9
Details	NDPK Nucleoside diphosphate kinase (NDPK) active site signature. NavHGSDSV

Chain	Residue	Details
A	ASN114-VAL122

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	ACT_SITE: Pros-phosphohistidine intermediate => ECO:0000255\|HAMAP-Rule:MF_00451

Chain	Residue	Details
A	HIS117
B	HIS117
C	HIS117
D	HIS117
E	HIS117
F	HIS117
G	HIS117
H	HIS117
I	HIS117
J	HIS117
K	HIS117
L	HIS117
M	HIS117
N	HIS117
O	HIS117
P	HIS117

site_id	SWS_FT_FI2
Number of Residues	96
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_00451

Chain	Residue	Details
A	LYS11
A	PHE59
A	ARG87
A	THR93
A	ARG104
A	ASN114
B	LYS11
B	PHE59
B	ARG87
B	THR93
B	ARG104
B	ASN114
C	LYS11
C	PHE59
C	ARG87
C	THR93
C	ARG104
C	ASN114
D	LYS11
D	PHE59
D	ARG87
D	THR93
D	ARG104
D	ASN114
E	LYS11
E	PHE59
E	ARG87
E	THR93
E	ARG104
E	ASN114
F	LYS11
F	PHE59
F	ARG87
F	THR93
F	ARG104
F	ASN114
G	LYS11
G	PHE59
G	ARG87
G	THR93
G	ARG104
G	ASN114
H	LYS11
H	PHE59
H	ARG87
H	THR93
H	ARG104
H	ASN114
I	LYS11
I	PHE59
I	ARG87
I	THR93
I	ARG104
I	ASN114
J	LYS11
J	PHE59
J	ARG87
J	THR93
J	ARG104
J	ASN114
K	LYS11
K	PHE59
K	ARG87
K	THR93
K	ARG104
K	ASN114
L	LYS11
L	PHE59
L	ARG87
L	THR93
L	ARG104
L	ASN114
M	LYS11
M	PHE59
M	ARG87
M	THR93
M	ARG104
M	ASN114
N	LYS11
N	PHE59
N	ARG87
N	THR93
N	ARG104
N	ASN114
O	LYS11
O	PHE59
O	ARG87
O	THR93
O	ARG104
O	ASN114
P	LYS11
P	PHE59
P	ARG87
P	THR93
P	ARG104
P	ASN114

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