Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2G82

High Resolution Structures of Thermus aquaticus Glyceraldehyde-3-Phosphate Dehydrogenase: Role of 220's Loop Motion in Catalysis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
A	0005737	cellular_component	cytoplasm
A	0006006	biological_process	glucose metabolic process
A	0006096	biological_process	glycolytic process
A	0016491	molecular_function	oxidoreductase activity
A	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
B	0000166	molecular_function	nucleotide binding
B	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B	0005737	cellular_component	cytoplasm
B	0006006	biological_process	glucose metabolic process
B	0006096	biological_process	glycolytic process
B	0016491	molecular_function	oxidoreductase activity
B	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
C	0000166	molecular_function	nucleotide binding
C	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
C	0005737	cellular_component	cytoplasm
C	0006006	biological_process	glucose metabolic process
C	0006096	biological_process	glycolytic process
C	0016491	molecular_function	oxidoreductase activity
C	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
D	0000166	molecular_function	nucleotide binding
D	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
D	0005737	cellular_component	cytoplasm
D	0006006	biological_process	glucose metabolic process
D	0006096	biological_process	glycolytic process
D	0016491	molecular_function	oxidoreductase activity
D	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
D	0050661	molecular_function	NADP binding
D	0051287	molecular_function	NAD binding
O	0000166	molecular_function	nucleotide binding
O	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
O	0005737	cellular_component	cytoplasm
O	0006006	biological_process	glucose metabolic process
O	0006096	biological_process	glycolytic process
O	0016491	molecular_function	oxidoreductase activity
O	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
O	0050661	molecular_function	NADP binding
O	0051287	molecular_function	NAD binding
P	0000166	molecular_function	nucleotide binding
P	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
P	0005737	cellular_component	cytoplasm
P	0006006	biological_process	glucose metabolic process
P	0006096	biological_process	glycolytic process
P	0016491	molecular_function	oxidoreductase activity
P	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
P	0050661	molecular_function	NADP binding
P	0051287	molecular_function	NAD binding
Q	0000166	molecular_function	nucleotide binding
Q	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
Q	0005737	cellular_component	cytoplasm
Q	0006006	biological_process	glucose metabolic process
Q	0006096	biological_process	glycolytic process
Q	0016491	molecular_function	oxidoreductase activity
Q	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
Q	0050661	molecular_function	NADP binding
Q	0051287	molecular_function	NAD binding
R	0000166	molecular_function	nucleotide binding
R	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
R	0005737	cellular_component	cytoplasm
R	0006006	biological_process	glucose metabolic process
R	0006096	biological_process	glycolytic process
R	0016491	molecular_function	oxidoreductase activity
R	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
R	0050661	molecular_function	NADP binding
R	0051287	molecular_function	NAD binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA C 1600

Chain	Residue
C	PGE1700
C	HOH1853
C	HOH1996
Q	HOH3563
Q	HOH3699

site_id	AC2
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD O 336

Chain	Residue
O	ILE11
O	ASN30
O	ASP31
O	LEU32
O	LYS75
O	SER93
O	THR94
O	GLY95
O	PHE97
O	THR117
O	ALA118
O	CSD149
O	ASN180
O	ASN311
O	TYR315
O	HOH341
O	HOH355
O	HOH368
O	HOH377
O	HOH384
O	HOH424
O	HOH431
O	HOH446
O	HOH469
O	HOH479
O	HOH521
R	LEU187
R	HOH3525
O	ASN6
O	GLY7
O	GLY9
O	ARG10

site_id	AC3
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD P 336

Chain	Residue
P	ASN6
P	GLY7
P	GLY9
P	ARG10
P	ILE11
P	ASN30
P	ASP31
P	LEU32
P	LYS75
P	SER93
P	THR94
P	GLY95
P	PHE97
P	THR117
P	ALA118
P	CSD149
P	ASN180
P	ASN311
P	TYR315
P	HOH337
P	HOH343
P	HOH351
P	HOH361
P	HOH369
P	HOH396
P	HOH404
P	HOH411
P	HOH417
P	HOH422
P	HOH455
P	HOH476
Q	LEU187
Q	HOH3520

site_id	AC4
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAD Q 336

Chain	Residue
Q	HOH3619
Q	HOH3631
Q	HOH3667
Q	HOH3681
Q	HOH3688
P	LEU187
P	HOH339
Q	ASN6
Q	GLY7
Q	GLY9
Q	ARG10
Q	ILE11
Q	ASN30
Q	ASP31
Q	LEU32
Q	LYS75
Q	SER93
Q	THR94
Q	GLY95
Q	PHE97
Q	THR117
Q	ALA118
Q	CSD149
Q	ASN180
Q	ASN311
Q	TYR315
Q	HOH3504
Q	HOH3508
Q	HOH3522
Q	HOH3541
Q	HOH3554
Q	HOH3590
Q	HOH3601
Q	HOH3603

site_id	AC5
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD R 336

Chain	Residue
O	LEU187
O	HOH347
R	ASN6
R	GLY7
R	GLY9
R	ARG10
R	ILE11
R	ASN30
R	ASP31
R	LEU32
R	LYS75
R	SER93
R	THR94
R	GLY95
R	PHE97
R	THR117
R	ALA118
R	CSD149
R	ASN180
R	ASN311
R	TYR315
R	HOH3504
R	HOH3505
R	HOH3508
R	HOH3544
R	HOH3548
R	HOH3573
R	HOH3593
R	HOH3599
R	HOH3607
R	HOH3653
R	HOH3666
R	HOH3672

site_id	AC6
Number of Residues	31
Details	BINDING SITE FOR RESIDUE NAD A 336

Chain	Residue
A	ASN6
A	GLY7
A	GLY9
A	ARG10
A	ILE11
A	ASP31
A	LEU32
A	LYS75
A	SER93
A	THR94
A	GLY95
A	PHE97
A	THR117
A	ALA118
A	CSD149
A	ASN180
A	ASN311
A	TYR315
A	HOH339
A	HOH345
A	HOH352
A	HOH365
A	HOH404
A	HOH429
A	HOH465
A	HOH466
A	HOH487
A	HOH501
A	HOH507
D	LEU187
D	HOH3519

site_id	AC7
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD B 336

Chain	Residue
B	ASN6
B	GLY7
B	GLY9
B	ARG10
B	ILE11
B	ASP31
B	LEU32
B	LYS75
B	SER93
B	THR94
B	GLY95
B	PHE97
B	THR117
B	ALA118
B	CSD149
B	ASN180
B	ASN311
B	TYR315
B	HOH340
B	HOH341
B	HOH356
B	HOH366
B	HOH370
B	HOH377
B	HOH395
B	HOH409
B	HOH410
B	HOH415
B	HOH449
B	HOH474
C	LEU187
C	HOH1824

site_id	AC8
Number of Residues	32
Details	BINDING SITE FOR RESIDUE NAD C 336

Chain	Residue
B	LEU187
B	HOH338
C	ASN6
C	GLY7
C	GLY9
C	ARG10
C	ILE11
C	ASN30
C	ASP31
C	LEU32
C	LYS75
C	SER93
C	THR94
C	GLY95
C	PHE97
C	THR117
C	ALA118
C	CSD149
C	ASN180
C	ASN311
C	TYR315
C	HOH1802
C	HOH1803
C	HOH1815
C	HOH1833
C	HOH1847
C	HOH1895
C	HOH1917
C	HOH1918
C	HOH1945
C	HOH1961
C	HOH1994

site_id	AC9
Number of Residues	30
Details	BINDING SITE FOR RESIDUE NAD D 336

Chain	Residue
A	LEU187
A	HOH346
D	ASN6
D	GLY7
D	GLY9
D	ARG10
D	ILE11
D	ASP31
D	LEU32
D	LYS75
D	SER93
D	THR94
D	GLY95
D	PHE97
D	THR117
D	ALA118
D	CSD149
D	ASN180
D	ASN311
D	TYR315
D	HOH3509
D	HOH3517
D	HOH3530
D	HOH3536
D	HOH3547
D	HOH3564
D	HOH3579
D	HOH3590
D	HOH3595
D	HOH3650

site_id	BC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PGE C 1700

Chain	Residue
C	ASP65
C	NA1600
C	HOH1853
C	HOH1996
C	HOH1998
Q	ASP65
Q	HOH3563
Q	HOH3699
Q	HOH3722

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IPA C 1800

Chain	Residue
C	HOH1862
Q	HOH3736
R	GLY222

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IPA Q 1801

Chain	Residue
D	GLY222
Q	GLU248
Q	HOH3546
Q	HOH3736

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL R 3502

Chain	Residue
Q	GLU276
Q	LYS294
Q	LEU295
R	ARG193
R	THR206
R	HOH3623

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL Q 3503

Chain	Residue
Q	ARG193
Q	THR206
R	GLU276
R	LYS294

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 3504

Chain	Residue
C	GLU276
C	LEU295
D	ARG193
D	THR205
D	THR206
D	MET227
D	HOH3637

Functional Information from PROSITE/UniProt

site_id	PS00071
Number of Residues	8
Details	GAPDH Glyceraldehyde 3-phosphate dehydrogenase active site. ASCTTNsL

Chain	Residue	Details
O	ALA147-LEU154

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"8611563","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8611563","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2006","submissionDatabase":"PDB data bank","title":"High resolution structures of Thermus aquaticus glyceraldehyde-3-phosphate dehydrogenase: role of 220's loop motion in catalysis.","authors":["Jenkins J.L.","Buencamino R.","Tanner J.J."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAR-2006","submissionDatabase":"PDB data bank","title":"High resolution structures of Thermus aquaticus glyceraldehyde-3-phosphate dehydrogenase: role of 220's loop motion in catalysis.","authors":["Jenkins J.L.","Buencamino R.","Tanner J.J."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P00362","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"PubMed","id":"8611563","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

Catalytic Information from CSA

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

Chain	Residue	Details
O	HIS176

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

Chain	Residue	Details
P	HIS176

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

Chain	Residue	Details
Q	HIS176

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

Chain	Residue	Details
R	HIS176

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

Chain	Residue	Details
A	HIS176

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

Chain	Residue	Details
B	HIS176

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

Chain	Residue	Details
C	HIS176

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

Chain	Residue	Details
D	HIS176

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