Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1YBA

The active form of phosphoglycerate dehydrogenase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004617	molecular_function	phosphoglycerate dehydrogenase activity
A	0005829	cellular_component	cytosol
A	0006564	biological_process	L-serine biosynthetic process
A	0008652	biological_process	amino acid biosynthetic process
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0042802	molecular_function	identical protein binding
A	0047545	molecular_function	(S)-2-hydroxyglutarate dehydrogenase activity
A	0051287	molecular_function	NAD binding
A	0070403	molecular_function	NAD+ binding
A	0070404	molecular_function	NADH binding
A	0070905	molecular_function	serine binding
A	0120568	molecular_function	(R)-2-hydroxyglutarate (NAD+) dehydrogenase activity
B	0004617	molecular_function	phosphoglycerate dehydrogenase activity
B	0005829	cellular_component	cytosol
B	0006564	biological_process	L-serine biosynthetic process
B	0008652	biological_process	amino acid biosynthetic process
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0042802	molecular_function	identical protein binding
B	0047545	molecular_function	(S)-2-hydroxyglutarate dehydrogenase activity
B	0051287	molecular_function	NAD binding
B	0070403	molecular_function	NAD+ binding
B	0070404	molecular_function	NADH binding
B	0070905	molecular_function	serine binding
B	0120568	molecular_function	(R)-2-hydroxyglutarate (NAD+) dehydrogenase activity
C	0004617	molecular_function	phosphoglycerate dehydrogenase activity
C	0005829	cellular_component	cytosol
C	0006564	biological_process	L-serine biosynthetic process
C	0008652	biological_process	amino acid biosynthetic process
C	0016491	molecular_function	oxidoreductase activity
C	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
C	0042802	molecular_function	identical protein binding
C	0047545	molecular_function	(S)-2-hydroxyglutarate dehydrogenase activity
C	0051287	molecular_function	NAD binding
C	0070403	molecular_function	NAD+ binding
C	0070404	molecular_function	NADH binding
C	0070905	molecular_function	serine binding
C	0120568	molecular_function	(R)-2-hydroxyglutarate (NAD+) dehydrogenase activity
D	0004617	molecular_function	phosphoglycerate dehydrogenase activity
D	0005829	cellular_component	cytosol
D	0006564	biological_process	L-serine biosynthetic process
D	0008652	biological_process	amino acid biosynthetic process
D	0016491	molecular_function	oxidoreductase activity
D	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
D	0042802	molecular_function	identical protein binding
D	0047545	molecular_function	(S)-2-hydroxyglutarate dehydrogenase activity
D	0051287	molecular_function	NAD binding
D	0070403	molecular_function	NAD+ binding
D	0070404	molecular_function	NADH binding
D	0070905	molecular_function	serine binding
D	0120568	molecular_function	(R)-2-hydroxyglutarate (NAD+) dehydrogenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 A 411

Chain	Residue
A	LEU142
A	ALA143
A	ALA144
A	HOH424
A	HOH446
A	HOH468
A	HOH565
B	ARG60

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 D 411

Chain	Residue
D	LEU142
D	ALA143
D	ALA144
D	HOH488
C	ARG60

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 C 411

Chain	Residue
C	LEU142
C	ALA143
C	ALA144
C	HOH432
C	HOH567
D	ARG60

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 B 411

Chain	Residue
A	ARG60
B	LEU142
B	ALA143
B	ALA144
B	HOH541
B	HOH557
B	HOH663

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 A 412

Chain	Residue
A	GLY85
A	THR86
A	ASN87
A	ARG240
A	HOH587

site_id	AC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE AKG A 413

Chain	Residue
A	ARG60
A	SER61
A	CYS83
A	ILE84
A	GLY85
A	HOH447
A	HOH488
A	HOH674
B	LYS141

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE AKG B 412

Chain	Residue
A	LYS141
B	SER61
B	CYS83
B	ILE84
B	ASN108
B	HOH417
B	HOH445
B	HOH538
B	HOH559
B	HOH720

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE AKG D 412

Chain	Residue
C	LYS141
D	ARG60
D	SER61
D	NAD415
D	HOH416
D	HOH630
D	HOH637
D	HOH679
D	HOH721

site_id	AC9
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AKG C 412

Chain	Residue
C	ARG60
C	SER61
C	CYS83
C	ILE84
C	ASN108
C	HOH439
C	HOH501
C	HOH503
C	HOH520
C	HOH585
C	HOH625
C	HOH636
D	LYS141

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE UNL A 414

Chain	Residue
A	TYR180
A	GLN195
A	HIS196
A	LEU197
A	SER198
A	HOH598
A	HOH645

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNL B 413

Chain	Residue
B	TYR180
B	HIS196
B	LEU197
B	SER198

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNL C 413

Chain	Residue
C	TYR180
C	GLN195
C	HIS196
C	LEU197
C	SER198
C	HOH654

site_id	BC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE UNL D 413

Chain	Residue
B	LYS39
D	TYR180
D	HIS196
D	LEU197
D	SER198
D	HOH550
D	HOH589
D	HOH763

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UNL A 415

Chain	Residue
A	GLY40
A	ALA41
A	LEU42
A	HOH678
A	HIS38
A	LYS39

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UNL C 414

Chain	Residue
C	HIS38
C	LYS39
C	GLY40

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UNL D 414

Chain	Residue
D	HIS38
D	LYS39
D	GLY40
D	ALA41

site_id	BC8
Number of Residues	29
Details	BINDING SITE FOR RESIDUE NAD A 416

Chain	Residue
A	ILE84
A	PHE106
A	VAL112
A	GLY158
A	TYR159
A	GLY160
A	HIS161
A	ILE162
A	ASP181
A	ILE182
A	LYS185
A	HIS210
A	VAL211
A	PRO212
A	SER216
A	THR217
A	MSE220
A	ALA238
A	SER239
A	ARG240
A	ASP264
A	HIS292
A	GLY294
A	GLY295
A	HOH433
A	HOH445
A	HOH450
A	HOH500
A	HOH521

site_id	BC9
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD B 414

Chain	Residue
B	ILE84
B	PHE106
B	VAL112
B	GLY158
B	TYR159
B	GLY160
B	HIS161
B	ILE162
B	TYR180
B	ASP181
B	ILE182
B	LYS185
B	HIS210
B	VAL211
B	PRO212
B	SER216
B	THR217
B	MSE220
B	ALA238
B	SER239
B	ARG240
B	ASP264
B	HIS292
B	GLY294
B	GLY295
B	HOH442
B	HOH454
B	HOH517
B	HOH548
B	HOH549
B	HOH569
B	HOH590
B	HOH737

site_id	CC1
Number of Residues	28
Details	BINDING SITE FOR RESIDUE NAD C 415

Chain	Residue
C	ILE84
C	PHE106
C	VAL112
C	GLY158
C	TYR159
C	GLY160
C	HIS161
C	ILE162
C	ASP181
C	ILE182
C	LYS185
C	HIS210
C	VAL211
C	PRO212
C	SER216
C	THR217
C	ALA238
C	SER239
C	ARG240
C	ASP264
C	HIS292
C	GLY294
C	GLY295
C	HOH421
C	HOH450
C	HOH469
C	HOH471
C	HOH662

site_id	CC2
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD D 415

Chain	Residue
D	ASN108
D	GLY158
D	TYR159
D	GLY160
D	HIS161
D	ILE162
D	TYR180
D	ASP181
D	ILE182
D	GLU183
D	LYS185
D	HIS210
D	VAL211
D	PRO212
D	SER216
D	THR217
D	ALA238
D	SER239
D	ARG240
D	ASP264
D	HIS292
D	GLY294
D	GLY295
D	AKG412
D	HOH416
D	HOH417
D	HOH482
D	HOH498
D	HOH570
D	HOH660
D	HOH701
D	HOH726
D	HOH769

Functional Information from PROSITE/UniProt

site_id	PS00065
Number of Residues	28
Details	D_2_HYDROXYACID_DH_1 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. LGIIGyGHIGtqlgilaeslgmy.VYfYD

Chain	Residue	Details
A	LEU154-ASP181

site_id	PS00670
Number of Residues	23
Details	D_2_HYDROXYACID_DH_2 D-isomer specific 2-hydroxyacid dehydrogenases signature 2. LLnmSDVVsLHvPenpsTknMmG

Chain	Residue	Details
A	LEU200-GLY222

site_id	PS00671
Number of Residues	17
Details	D_2_HYDROXYACID_DH_3 D-isomer specific 2-hydroxyacid dehydrogenases signature 3. MKpGsLLINaSRGtVVD

Chain	Residue	Details
A	MSE229-ASP245

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton donor"}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"PubMed","id":"7719856","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1psd

Chain	Residue	Details
A	GLU269
A	HIS292

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1psd

Chain	Residue	Details
B	GLU269
B	HIS292

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1psd

Chain	Residue	Details
C	GLU269
C	HIS292

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1psd

Chain	Residue	Details
D	GLU269
D	HIS292

site_id	MCSA1
Number of Residues	2
Details	M-CSA 785

Chain	Residue	Details
A	LEU289	electrostatic stabiliser
A	LEU312	proton acceptor, proton donor

site_id	MCSA2
Number of Residues	2
Details	M-CSA 785

Chain	Residue	Details
B	LEU289	electrostatic stabiliser
B	LEU312	proton acceptor, proton donor

site_id	MCSA3
Number of Residues	2
Details	M-CSA 785

Chain	Residue	Details
C	LEU289	electrostatic stabiliser
C	LEU312	proton acceptor, proton donor

site_id	MCSA4
Number of Residues	2
Details	M-CSA 785

Chain	Residue	Details
D	LEU289	electrostatic stabiliser
D	LEU312	proton acceptor, proton donor

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