Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2JKV

Structure of human Phosphogluconate Dehydrogenase in complex with NADPH at 2.53A

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004616	molecular_function	phosphogluconate dehydrogenase (decarboxylating) activity
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006098	biological_process	pentose-phosphate shunt
A	0006739	biological_process	NADP+ metabolic process
A	0006740	biological_process	NADPH regeneration
A	0009051	biological_process	pentose-phosphate shunt, oxidative branch
A	0016491	molecular_function	oxidoreductase activity
A	0019322	biological_process	pentose biosynthetic process
A	0019521	biological_process	D-gluconate metabolic process
A	0030246	molecular_function	carbohydrate binding
A	0031406	molecular_function	carboxylic acid binding
A	0050661	molecular_function	NADP binding
A	0070062	cellular_component	extracellular exosome
B	0004616	molecular_function	phosphogluconate dehydrogenase (decarboxylating) activity
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006098	biological_process	pentose-phosphate shunt
B	0006739	biological_process	NADP+ metabolic process
B	0006740	biological_process	NADPH regeneration
B	0009051	biological_process	pentose-phosphate shunt, oxidative branch
B	0016491	molecular_function	oxidoreductase activity
B	0019322	biological_process	pentose biosynthetic process
B	0019521	biological_process	D-gluconate metabolic process
B	0030246	molecular_function	carbohydrate binding
B	0031406	molecular_function	carboxylic acid binding
B	0050661	molecular_function	NADP binding
B	0070062	cellular_component	extracellular exosome
C	0004616	molecular_function	phosphogluconate dehydrogenase (decarboxylating) activity
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006098	biological_process	pentose-phosphate shunt
C	0006739	biological_process	NADP+ metabolic process
C	0006740	biological_process	NADPH regeneration
C	0009051	biological_process	pentose-phosphate shunt, oxidative branch
C	0016491	molecular_function	oxidoreductase activity
C	0019322	biological_process	pentose biosynthetic process
C	0019521	biological_process	D-gluconate metabolic process
C	0030246	molecular_function	carbohydrate binding
C	0031406	molecular_function	carboxylic acid binding
C	0050661	molecular_function	NADP binding
C	0070062	cellular_component	extracellular exosome
D	0004616	molecular_function	phosphogluconate dehydrogenase (decarboxylating) activity
D	0005634	cellular_component	nucleus
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006098	biological_process	pentose-phosphate shunt
D	0006739	biological_process	NADP+ metabolic process
D	0006740	biological_process	NADPH regeneration
D	0009051	biological_process	pentose-phosphate shunt, oxidative branch
D	0016491	molecular_function	oxidoreductase activity
D	0019322	biological_process	pentose biosynthetic process
D	0019521	biological_process	D-gluconate metabolic process
D	0030246	molecular_function	carbohydrate binding
D	0031406	molecular_function	carboxylic acid binding
D	0050661	molecular_function	NADP binding
D	0070062	cellular_component	extracellular exosome
E	0004616	molecular_function	phosphogluconate dehydrogenase (decarboxylating) activity
E	0005634	cellular_component	nucleus
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006098	biological_process	pentose-phosphate shunt
E	0006739	biological_process	NADP+ metabolic process
E	0006740	biological_process	NADPH regeneration
E	0009051	biological_process	pentose-phosphate shunt, oxidative branch
E	0016491	molecular_function	oxidoreductase activity
E	0019322	biological_process	pentose biosynthetic process
E	0019521	biological_process	D-gluconate metabolic process
E	0030246	molecular_function	carbohydrate binding
E	0031406	molecular_function	carboxylic acid binding
E	0050661	molecular_function	NADP binding
E	0070062	cellular_component	extracellular exosome
F	0004616	molecular_function	phosphogluconate dehydrogenase (decarboxylating) activity
F	0005634	cellular_component	nucleus
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006098	biological_process	pentose-phosphate shunt
F	0006739	biological_process	NADP+ metabolic process
F	0006740	biological_process	NADPH regeneration
F	0009051	biological_process	pentose-phosphate shunt, oxidative branch
F	0016491	molecular_function	oxidoreductase activity
F	0019322	biological_process	pentose biosynthetic process
F	0019521	biological_process	D-gluconate metabolic process
F	0030246	molecular_function	carbohydrate binding
F	0031406	molecular_function	carboxylic acid binding
F	0050661	molecular_function	NADP binding
F	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAP A 500

Chain	Residue
A	GLY451
A	HOH2256
A	HOH2257
A	HOH2258
B	GLY10
B	LEU11
B	ALA12
B	VAL13
B	MET14
B	ASN33
B	ARG34
A	HIS453
B	THR35
B	LYS38
B	LEU74
B	VAL75
B	LYS76
B	ALA77
B	ALA80
B	PHE84
B	GLY102
B	ASN103
A	SER478
B	VAL128
B	GLY131
B	CL1484
B	HOH2046
B	HOH2049
A	SER479
A	TYR481
A	HOH2252
A	HOH2253
A	HOH2254
A	HOH2255

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 1484

Chain	Residue
A	ASN103
A	LYS184
A	ASN188
B	NAP500

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 A 1485

Chain	Residue
A	TYR192
A	GLN260
A	LYS261
A	ARG288
A	HOH2160
A	HOH2259
A	HOH2260
A	HOH2261
B	ARG447
B	HIS453

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 1486

Chain	Residue
A	LYS248
A	HIS249
A	HOH2262
A	HOH2263

site_id	AC5
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAP B 500

Chain	Residue
A	GLY10
A	LEU11
A	ALA12
A	VAL13
A	MET14
A	ASN33
A	ARG34
A	THR35
A	LYS38
A	LEU74
A	VAL75
A	LYS76
A	ALA77
A	ALA80
A	PHE84
A	GLY102
A	ASN103
A	VAL128
A	GLY131
A	CL1484
A	HOH2014
A	HOH2039
B	GLY451
B	SER478
B	SER479
B	TYR481
B	HOH2262
B	HOH2263
B	HOH2264
B	HOH2265

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL B 1484

Chain	Residue
A	NAP500
B	ASN103
B	LYS184
B	ASN188

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL B 1485

Chain	Residue
B	TRP150
B	LYS154

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 B 1486

Chain	Residue
A	ARG447
B	TYR192
B	GLN260
B	LYS261
B	ARG288
B	HOH2165
B	HOH2266
B	HOH2267

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 1487

Chain	Residue
B	HOH2269
B	LYS248
B	HIS249
B	HOH2158

site_id	BC1
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAP C 500

Chain	Residue
C	GLY451
C	HIS453
C	SER478
C	SER479
C	TYR481
C	HOH2191
C	HOH2192
C	HOH2193
C	HOH2194
D	GLY10
D	LEU11
D	ALA12
D	VAL13
D	MET14
D	ASN33
D	ARG34
D	THR35
D	LYS38
D	LEU74
D	VAL75
D	LYS76
D	ALA77
D	ALA80
D	PHE84
D	GLY102
D	ASN103
D	VAL128
D	GLY131
D	CL1486
D	HOH2053
D	HOH2054
D	HOH2133

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 1484

Chain	Residue
C	TYR192
C	GLN260
C	LYS261
C	ARG288
C	HOH2106
C	HOH2127
C	HOH2195
D	ARG447

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 C 1485

Chain	Residue
C	LYS248
C	HIS249

site_id	BC4
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAP D 500

Chain	Residue
C	GLY10
C	LEU11
C	ALA12
C	VAL13
C	MET14
C	ASN33
C	ARG34
C	THR35
C	LYS38
C	LEU74
C	VAL75
C	LYS76
C	ALA77
C	ALA80
C	PHE84
C	GLY102
C	ASN103
C	VAL128
C	GLY131
C	HOH2011
C	HOH2032
D	GLY451
D	HIS453
D	SER478
D	SER479
D	TYR481
D	HOH2184
D	HOH2188
D	HOH2189
D	HOH2190

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 1484

Chain	Residue
C	ARG447
C	HIS453
D	TYR192
D	LYS261
D	ARG288
D	HOH2113
D	HOH2134
D	HOH2191

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 1485

Chain	Residue
D	LYS248
D	HIS249
D	HOH2130

site_id	BC7
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAP E 500

Chain	Residue
E	GLY451
E	HIS453
E	SER478
E	SER479
E	TYR481
E	HOH2226
E	HOH2232
E	HOH2233
E	HOH2234
E	HOH2235
F	GLY10
F	LEU11
F	ALA12
F	VAL13
F	MET14
F	ASN33
F	ARG34
F	THR35
F	LYS38
F	LEU74
F	VAL75
F	LYS76
F	ALA77
F	ALA80
F	PHE84
F	GLY102
F	ASN103
F	VAL128
F	GLY131
F	CL1473
F	HOH2050
F	HOH2054
F	HOH2159

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 1484

Chain	Residue
E	LYS248
E	HIS249
E	HOH2237

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 E 1485

Chain	Residue
E	TYR192
E	LYS261
E	ARG288
E	HOH2238
F	ARG447

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL F 1473

Chain	Residue
E	NAP500
F	ASN103
F	LYS184
F	ASN188
F	HOH2247

site_id	CC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 F 1474

Chain	Residue
E	ARG447
E	HIS453
F	TYR192
F	GLN260
F	LYS261
F	ARG288
F	HOH2160
F	HOH2247
F	HOH2248

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 F 1475

Chain	Residue
F	LYS248
F	HIS249
F	HOH2249

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL F 1476

Chain	Residue
F	HOH2106
F	HOH2110
F	HOH2118

site_id	CC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL A 1488

Chain	Residue
A	LYS303

site_id	CC6
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL E 1486

Chain	Residue
E	TRP150

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL A 1487

Chain	Residue
A	TRP150
A	LYS154
A	ASP172
A	HOH2096

site_id	CC8
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL B 1488

Chain	Residue
B	LYS303
B	HOH2174

site_id	CC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL E 1488

Chain	Residue
F	LYS396

site_id	DC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL D 1486

Chain	Residue
C	NAP500
D	SER129
D	LYS184
D	ILE367
D	HOH2112

Functional Information from PROSITE/UniProt

site_id	PS00461
Number of Residues	13
Details	6PGD 6-phosphogluconate dehydrogenase signature. IrDsaGQKGTGkW

Chain	Residue	Details
A	ILE254-TRP266

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Proton acceptor","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	54
Details	Binding site: {"description":"in other chain","evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2009","submissionDatabase":"PDB data bank","title":"Structure of human phosphogluconate dehydrogenase in complex with NADPH at 2.53 A.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	42
Details	Binding site: {"description":"in other chain","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	12
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2009","submissionDatabase":"PDB data bank","title":"Structure of human phosphogluconate dehydrogenase in complex with NADPH at 2.53 A.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"Q9DCD0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	12
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"Q9DCD0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	12
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	4
Details	Annotated By Reference To The Literature 2pgd

Chain	Residue	Details
A	GLY131
A	GLU191
A	LYS184
A	ASN188

site_id	CSA2
Number of Residues	4
Details	Annotated By Reference To The Literature 2pgd

Chain	Residue	Details
B	GLY131
B	GLU191
B	LYS184
B	ASN188

site_id	CSA3
Number of Residues	4
Details	Annotated By Reference To The Literature 2pgd

Chain	Residue	Details
C	GLY131
C	GLU191
C	LYS184
C	ASN188

site_id	CSA4
Number of Residues	4
Details	Annotated By Reference To The Literature 2pgd

Chain	Residue	Details
D	GLY131
D	GLU191
D	LYS184
D	ASN188

site_id	CSA5
Number of Residues	4
Details	Annotated By Reference To The Literature 2pgd

Chain	Residue	Details
E	GLY131
E	GLU191
E	LYS184
E	ASN188

site_id	CSA6
Number of Residues	4
Details	Annotated By Reference To The Literature 2pgd

Chain	Residue	Details
F	GLY131
F	GLU191
F	LYS184
F	ASN188

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