Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2DBR

Crystal Structure of Glyoxylate Reductase (PH0597) from Pyrococcus horikoshii OT3, Complexed with NADP (P1)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
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	0016618	molecular_function	hydroxypyruvate reductase [NAD(P)H] activity
A	0030267	molecular_function	glyoxylate reductase (NADPH) activity
A	0047964	molecular_function	glyoxylate reductase (NADH) activity
A	0051287	molecular_function	NAD binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
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	0016618	molecular_function	hydroxypyruvate reductase [NAD(P)H] activity
B	0030267	molecular_function	glyoxylate reductase (NADPH) activity
B	0047964	molecular_function	glyoxylate reductase (NADH) activity
B	0051287	molecular_function	NAD binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
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	0016618	molecular_function	hydroxypyruvate reductase [NAD(P)H] activity
C	0030267	molecular_function	glyoxylate reductase (NADPH) activity
C	0047964	molecular_function	glyoxylate reductase (NADH) activity
C	0051287	molecular_function	NAD binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
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	0016618	molecular_function	hydroxypyruvate reductase [NAD(P)H] activity
D	0030267	molecular_function	glyoxylate reductase (NADPH) activity
D	0047964	molecular_function	glyoxylate reductase (NADH) activity
D	0051287	molecular_function	NAD binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0016491	molecular_function	oxidoreductase activity
E	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
E	0016618	molecular_function	hydroxypyruvate reductase [NAD(P)H] activity
E	0030267	molecular_function	glyoxylate reductase (NADPH) activity
E	0047964	molecular_function	glyoxylate reductase (NADH) activity
E	0051287	molecular_function	NAD binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0016491	molecular_function	oxidoreductase activity
F	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
F	0016618	molecular_function	hydroxypyruvate reductase [NAD(P)H] activity
F	0030267	molecular_function	glyoxylate reductase (NADPH) activity
F	0047964	molecular_function	glyoxylate reductase (NADH) activity
F	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 501

Chain	Residue
A	TYR78
A	ASN95
A	ARG160
A	NAP401

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 502

Chain	Residue
C	TYR78
C	ASN95
C	ARG160

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 503

Chain	Residue
B	ARG160
B	NAP402
B	HOH513
B	TYR78
B	ASN95

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 504

Chain	Residue
D	TYR78
D	ASN95
D	ARG160
D	HOH524

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 505

Chain	Residue
E	TYR78
E	ASN95
E	ARG160
E	VAL321

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 F 506

Chain	Residue
F	TYR78
F	ASN95
F	ARG160

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 507

Chain	Residue
A	LEU53
A	ALA75
A	VAL76
A	GLY77
A	ARG241
A	HIS288
A	NAP401

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 C 508

Chain	Residue
C	LEU53
C	ALA75
C	VAL76
C	GLY77
C	ARG241
C	HIS288
C	NAP403

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 509

Chain	Residue
B	LEU53
B	ALA75
B	VAL76
B	GLY77
B	ARG241
B	NAP402

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 D 510

Chain	Residue
D	LEU53
D	ALA75
D	VAL76
D	LEU100
D	ARG241
D	NAP404

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 E 511

Chain	Residue
E	LEU53
E	ALA75
E	VAL76
E	GLY77
E	LEU100
E	ARG241
E	HIS288
E	NAP405

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 F 512

Chain	Residue
F	LEU53
F	ALA75
F	VAL76
F	GLY77
F	ARG241
F	SER291
F	NAP406

site_id	BC4
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAP A 401

Chain	Residue
A	VAL76
A	THR104
A	LEU158
A	GLY159
A	ARG160
A	ILE161
A	SER180
A	ARG181
A	PRO213
A	THR218
A	ILE239
A	ALA240
A	ARG241
A	ASP265
A	HIS288
A	GLY290
A	SER291
A	SO4501
A	SO4507
A	HOH508
C	LYS42

site_id	BC5
Number of Residues	27
Details	BINDING SITE FOR RESIDUE NAP B 402

Chain	Residue
B	ALA240
B	ARG241
B	ASP265
B	VAL266
B	HIS288
B	GLY290
B	SER291
B	SO4503
B	SO4509
B	HOH511
B	HOH513
B	HOH520
D	LYS42
B	VAL76
B	GLY77
B	THR104
B	LEU158
B	GLY159
B	ARG160
B	ILE161
B	SER180
B	ARG181
B	ALA211
B	VAL212
B	PRO213
B	THR218
B	ILE239

site_id	BC6
Number of Residues	24
Details	BINDING SITE FOR RESIDUE NAP C 403

Chain	Residue
C	VAL76
C	GLY77
C	THR104
C	GLY157
C	LEU158
C	GLY159
C	ARG160
C	ILE161
C	TYR179
C	SER180
C	ARG181
C	THR182
C	VAL212
C	PRO213
C	THR218
C	ILE239
C	ALA240
C	ARG241
C	ASP265
C	HIS288
C	GLY290
C	SER291
C	SO4508
C	HOH513

site_id	BC7
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAP D 404

Chain	Residue
D	VAL76
D	LEU100
D	THR104
D	LEU158
D	GLY159
D	ARG160
D	ILE161
D	SER180
D	ARG181
D	THR182
D	PRO213
D	GLU217
D	THR218
D	ILE239
D	ALA240
D	ARG241
D	ASP265
D	VAL266
D	HIS288
D	GLY290
D	SER291
D	SO4510
D	HOH516

site_id	BC8
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAP E 405

Chain	Residue
E	VAL76
E	GLY77
E	THR104
E	GLY157
E	LEU158
E	GLY159
E	ARG160
E	ILE161
E	TYR179
E	SER180
E	ARG181
E	THR182
E	LYS184
E	ALA211
E	VAL212
E	PRO213
E	THR218
E	ILE239
E	ARG241
E	ASP265
E	VAL266
E	HIS288
E	GLY290
E	SER291
E	SO4511
E	HOH514

site_id	BC9
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAP F 406

Chain	Residue
F	VAL76
F	THR104
F	LEU158
F	GLY159
F	ARG160
F	ILE161
F	SER180
F	ARG181
F	THR182
F	LYS184
F	ALA211
F	PRO213
F	THR218
F	ILE239
F	ALA240
F	ARG241
F	ASP265
F	VAL266
F	HIS288
F	GLY290
F	SER291
F	SO4512
F	HOH515

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. IGIIGlGRIGqaiakrakgfnmr.ILyYS

Chain	Residue	Details
A	ILE153-SER180

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

Chain	Residue	Details
A	MET230-ASP246

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Active site: {"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: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JUN-2006","submissionDatabase":"PDB data bank","title":"Crystal structure of glyoxylate reductase (ph0597) from Pyrococcus horikoshii OT3, complexed with nadp (i41).","authoringGroup":["RIKEN structural genomics initiative (RSGI)"]}}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	5
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
A	LYS243
A	ASP265
A	ARG241
A	GLU270
A	HIS288

site_id	CSA10
Number of Residues	2
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
D	GLU270
D	HIS288

site_id	CSA11
Number of Residues	2
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
E	GLU270
E	HIS288

site_id	CSA12
Number of Residues	2
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
F	GLU270
F	HIS288

site_id	CSA2
Number of Residues	5
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
B	LYS243
B	ASP265
B	ARG241
B	GLU270
B	HIS288

site_id	CSA3
Number of Residues	5
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
C	LYS243
C	ASP265
C	ARG241
C	GLU270
C	HIS288

site_id	CSA4
Number of Residues	5
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
D	LYS243
D	ASP265
D	ARG241
D	GLU270
D	HIS288

site_id	CSA5
Number of Residues	5
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
E	LYS243
E	ASP265
E	ARG241
E	GLU270
E	HIS288

site_id	CSA6
Number of Residues	5
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
F	LYS243
F	ASP265
F	ARG241
F	GLU270
F	HIS288

site_id	CSA7
Number of Residues	2
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
A	GLU270
A	HIS288

site_id	CSA8
Number of Residues	2
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
B	GLU270
B	HIS288

site_id	CSA9
Number of Residues	2
Details	Annotated By Reference To The Literature 1gdh

Chain	Residue	Details
C	GLU270
C	HIS288

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