7JWK

Crystal Structure of Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) from Mycoplasma genitalium with bound NAD

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	0006735	biological_process	NADH regeneration
A	0009986	cellular_component	cell surface
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	0044650	biological_process	adhesion of symbiont to host cell
A	0050661	molecular_function	NADP binding
A	0051287	molecular_function	NAD binding
A	0140032	molecular_function	glycosylation-dependent protein 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	0006735	biological_process	NADH regeneration
B	0009986	cellular_component	cell surface
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	0044650	biological_process	adhesion of symbiont to host cell
B	0050661	molecular_function	NADP binding
B	0051287	molecular_function	NAD binding
B	0140032	molecular_function	glycosylation-dependent protein 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	0006735	biological_process	NADH regeneration
C	0009986	cellular_component	cell surface
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	0044650	biological_process	adhesion of symbiont to host cell
C	0050661	molecular_function	NADP binding
C	0051287	molecular_function	NAD binding
C	0140032	molecular_function	glycosylation-dependent protein 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	0006735	biological_process	NADH regeneration
D	0009986	cellular_component	cell surface
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	0044650	biological_process	adhesion of symbiont to host cell
D	0050661	molecular_function	NADP binding
D	0051287	molecular_function	NAD binding
D	0140032	molecular_function	glycosylation-dependent protein binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	33
Details	binding site for residue NAD A 401

Chain	Residue
A	GLY14
A	SER101
A	THR102
A	GLY103
A	SER125
A	ALA126
A	CYS157
A	ALA188
A	ASN319
A	TYR323
A	PO4403
A	GLY16
A	HOH510
A	HOH512
A	HOH513
A	HOH526
A	HOH533
A	HOH552
A	HOH559
A	HOH565
A	HOH568
A	HOH575
A	ARG17
A	HOH577
A	HOH581
A	HOH592
A	HOH610
A	ILE18
A	ASN38
A	ASP39
A	LEU40
A	GLU82
A	LYS83

---

site_id	AC2
Number of Residues	11
Details	binding site for residue PO4 A 402

Chain	Residue
A	SER156
A	CYS157
A	THR158
A	HIS184
A	THR215
A	GLY216
A	PO4403
A	HOH544
A	HOH563
A	HOH575
A	HOH579

---

site_id	AC3
Number of Residues	9
Details	binding site for residue PO4 A 403

Chain	Residue
A	THR187
A	ARG202
A	ARG238
A	NAD401
A	PO4402
A	HOH501
A	HOH505
A	HOH526
A	HOH544

---

site_id	AC4
Number of Residues	5
Details	binding site for residue PEG A 404

Chain	Residue
A	LYS275
A	CYS277
A	ASP285
A	SER289
D	TYR52

---

site_id	AC5
Number of Residues	31
Details	binding site for residue NAD B 401

Chain	Residue
B	GLY14
B	GLY16
B	ARG17
B	ILE18
B	ASP39
B	LEU40
B	LYS83
B	SER101
B	THR102
B	GLY103
B	ARG104
B	PHE105
B	SER125
B	ALA126
B	CYS157
B	ALA188
B	ASN319
B	TYR323
B	PO4403
B	HOH508
B	HOH522
B	HOH543
B	HOH548
B	HOH549
B	HOH552
B	HOH557
B	HOH564
B	HOH587
B	HOH588
B	HOH604
D	HOH520

---

site_id	AC6
Number of Residues	10
Details	binding site for residue PO4 B 402

Chain	Residue
B	SER156
B	CYS157
B	THR158
B	HIS184
B	THR215
B	GLY216
B	HOH529
B	HOH537
B	HOH551
B	HOH587

---

site_id	AC7
Number of Residues	9
Details	binding site for residue PO4 B 403

Chain	Residue
B	THR187
B	ASP189
B	ARG202
B	ARG238
B	NAD401
B	HOH502
B	HOH513
B	HOH529
B	HOH545

---

site_id	AC8
Number of Residues	7
Details	binding site for residue PEG B 404

Chain	Residue
B	LYS275
B	CYS277
B	ASP285
B	SER289
B	ILE294
C	TYR52
C	GLU58

---

site_id	AC9
Number of Residues	33
Details	binding site for residue NAD C 401

Chain	Residue
C	GLY14
C	GLY16
C	ARG17
C	ILE18
C	ASN38
C	ASP39
C	LEU40
C	GLU82
C	LYS83
C	SER101
C	THR102
C	GLY103
C	ARG104
C	PHE105
C	SER125
C	ALA126
C	CYS157
C	ALA188
C	ASN319
C	TYR323
C	PO4403
C	HOH520
C	HOH532
C	HOH534
C	HOH543
C	HOH544
C	HOH549
C	HOH554
C	HOH558
C	HOH563
C	HOH568
C	HOH571
C	HOH579

---

site_id	AD1
Number of Residues	10
Details	binding site for residue PO4 C 402

Chain	Residue
C	SER156
C	CYS157
C	THR158
C	HIS184
C	THR215
C	GLY216
C	HOH512
C	HOH523
C	HOH553
C	HOH568

---

site_id	AD2
Number of Residues	9
Details	binding site for residue PO4 C 403

Chain	Residue
C	THR187
C	ASP189
C	ARG202
C	ARG238
C	NAD401
C	HOH501
C	HOH512
C	HOH526
C	HOH545

---

site_id	AD3
Number of Residues	4
Details	binding site for residue PEG C 404

Chain	Residue
C	LYS275
C	CYS277
C	ASP285
C	SER289

---

site_id	AD4
Number of Residues	26
Details	binding site for residue NAD D 401

Chain	Residue
B	HOH519
D	GLY14
D	GLY16
D	ARG17
D	ILE18
D	ASN38
D	ASP39
D	LEU40
D	LYS83
D	SER101
D	THR102
D	GLY103
D	PHE105
D	SER125
D	ALA126
D	CYS157
D	ALA188
D	ASN319
D	PO4403
D	HOH503
D	HOH508
D	HOH514
D	HOH527
D	HOH528
D	HOH529
D	HOH558

---

site_id	AD5
Number of Residues	10
Details	binding site for residue PO4 D 402

Chain	Residue
D	SER156
D	CYS157
D	THR158
D	HIS184
D	THR215
D	GLY216
D	PO4403
D	HOH506
D	HOH508
D	HOH509

---

site_id	AD6
Number of Residues	10
Details	binding site for residue PO4 D 403

Chain	Residue
D	THR187
D	ASP189
D	ARG202
D	ARG238
D	NAD401
D	PO4402
D	HOH501
D	HOH506
D	HOH508
D	HOH556

---

site_id	AD7
Number of Residues	3
Details	binding site for residue PEG D 404

Chain	Residue
D	CYS277
D	ASP285
D	SER289

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ALA155-LEU162

---

site_id	PS00584
Number of Residues	14
Details	PFKB_KINASES_2 pfkB family of carbohydrate kinases signature 2. KTiSSDDkiiSAAS

Chain	Residue	Details
A	LYS143-SER156

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Nucleophile => ECO:0000250|UniProtKB:P00362

Chain	Residue	Details
A	CYS157
B	CYS157
C	CYS157
D	CYS157

---

site_id	SWS_FT_FI2
Number of Residues	40
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P00362

Chain	Residue	Details
A	SER156
A	THR187
A	ARG202
A	THR215
A	ARG238
A	ASN319
B	ARG17
B	ASP39
B	LYS83
B	SER125
B	SER156
B	THR187
B	ARG202
B	THR215
B	ARG238
B	ASN319
C	ARG17
C	ASP39
C	LYS83
C	SER125
C	SER156
C	THR187
C	ARG202
C	THR215
C	ARG238
C	ASN319
D	ARG17
D	ASP39
D	LYS83
D	SER125
D	SER156
D	THR187
D	ARG202
D	THR215
D	ARG238
D	ASN319
A	ASP39
A	LYS83
A	SER125
A	ARG17

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	SITE: Activates thiol group during catalysis => ECO:0000250|UniProtKB:P00362

Chain	Residue	Details
D	HIS184
A	HIS184
B	HIS184
C	HIS184

---