5DDI

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase from pig muscle - holo enzyme - at 2.40 Angstrom resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
P	0000226	biological_process	microtubule cytoskeleton organization
P	0001819	biological_process	positive regulation of cytokine production
P	0002376	biological_process	immune system process
P	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
P	0005634	cellular_component	nucleus
P	0005737	cellular_component	cytoplasm
P	0005811	cellular_component	lipid droplet
P	0005829	cellular_component	cytosol
P	0005856	cellular_component	cytoskeleton
P	0005886	cellular_component	plasma membrane
P	0006006	biological_process	glucose metabolic process
P	0006096	biological_process	glycolytic process
P	0006417	biological_process	regulation of translation
P	0006915	biological_process	apoptotic process
P	0008017	molecular_function	microtubule binding
P	0015630	cellular_component	microtubule cytoskeleton
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	0016740	molecular_function	transferase activity
P	0017148	biological_process	negative regulation of translation
P	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
P	0031640	biological_process	killing of cells of another organism
P	0031965	cellular_component	nuclear membrane
P	0032481	biological_process	positive regulation of type I interferon production
P	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
P	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
P	0042802	molecular_function	identical protein binding
P	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
P	0043231	cellular_component	intracellular membrane-bounded organelle
P	0045087	biological_process	innate immune response
P	0050661	molecular_function	NADP binding
P	0050821	biological_process	protein stabilization
P	0050832	biological_process	defense response to fungus
P	0051287	molecular_function	NAD binding
P	0051402	biological_process	neuron apoptotic process
P	0051873	biological_process	killing by host of symbiont cells
P	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
P	0071346	biological_process	cellular response to type II interferon
P	0097452	cellular_component	GAIT complex
P	0097718	molecular_function	disordered domain specific binding
P	1990904	cellular_component	ribonucleoprotein complex
R	0000226	biological_process	microtubule cytoskeleton organization
R	0001819	biological_process	positive regulation of cytokine production
R	0002376	biological_process	immune system process
R	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
R	0005634	cellular_component	nucleus
R	0005737	cellular_component	cytoplasm
R	0005811	cellular_component	lipid droplet
R	0005829	cellular_component	cytosol
R	0005856	cellular_component	cytoskeleton
R	0005886	cellular_component	plasma membrane
R	0006006	biological_process	glucose metabolic process
R	0006096	biological_process	glycolytic process
R	0006417	biological_process	regulation of translation
R	0006915	biological_process	apoptotic process
R	0008017	molecular_function	microtubule binding
R	0015630	cellular_component	microtubule cytoskeleton
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	0016740	molecular_function	transferase activity
R	0017148	biological_process	negative regulation of translation
R	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
R	0031640	biological_process	killing of cells of another organism
R	0031965	cellular_component	nuclear membrane
R	0032481	biological_process	positive regulation of type I interferon production
R	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
R	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
R	0042802	molecular_function	identical protein binding
R	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
R	0043231	cellular_component	intracellular membrane-bounded organelle
R	0045087	biological_process	innate immune response
R	0050661	molecular_function	NADP binding
R	0050821	biological_process	protein stabilization
R	0050832	biological_process	defense response to fungus
R	0051287	molecular_function	NAD binding
R	0051402	biological_process	neuron apoptotic process
R	0051873	biological_process	killing by host of symbiont cells
R	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
R	0071346	biological_process	cellular response to type II interferon
R	0097452	cellular_component	GAIT complex
R	0097718	molecular_function	disordered domain specific binding
R	1990904	cellular_component	ribonucleoprotein complex
S	0000226	biological_process	microtubule cytoskeleton organization
S	0001819	biological_process	positive regulation of cytokine production
S	0002376	biological_process	immune system process
S	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
S	0005634	cellular_component	nucleus
S	0005737	cellular_component	cytoplasm
S	0005811	cellular_component	lipid droplet
S	0005829	cellular_component	cytosol
S	0005856	cellular_component	cytoskeleton
S	0005886	cellular_component	plasma membrane
S	0006006	biological_process	glucose metabolic process
S	0006096	biological_process	glycolytic process
S	0006417	biological_process	regulation of translation
S	0006915	biological_process	apoptotic process
S	0008017	molecular_function	microtubule binding
S	0015630	cellular_component	microtubule cytoskeleton
S	0016491	molecular_function	oxidoreductase activity
S	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
S	0016740	molecular_function	transferase activity
S	0017148	biological_process	negative regulation of translation
S	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
S	0031640	biological_process	killing of cells of another organism
S	0031965	cellular_component	nuclear membrane
S	0032481	biological_process	positive regulation of type I interferon production
S	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
S	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
S	0042802	molecular_function	identical protein binding
S	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
S	0043231	cellular_component	intracellular membrane-bounded organelle
S	0045087	biological_process	innate immune response
S	0050661	molecular_function	NADP binding
S	0050821	biological_process	protein stabilization
S	0050832	biological_process	defense response to fungus
S	0051287	molecular_function	NAD binding
S	0051402	biological_process	neuron apoptotic process
S	0051873	biological_process	killing by host of symbiont cells
S	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
S	0071346	biological_process	cellular response to type II interferon
S	0097452	cellular_component	GAIT complex
S	0097718	molecular_function	disordered domain specific binding
S	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	binding site for residue SO4 P 501

Chain	Residue
P	SER148
P	THR208
P	GLY209
P	ALA210
P	HOH620
P	HOH640

---

site_id	AC2
Number of Residues	3
Details	binding site for residue SO4 P 502

Chain	Residue
P	THR179
P	THR181
P	ARG231

---

site_id	AC3
Number of Residues	16
Details	binding site for residue NAD P 503

Chain	Residue
P	PHE8
P	GLY9
P	ARG10
P	ILE11
P	ASP32
P	PRO33
P	PHE34
P	ARG77
P	THR96
P	GLY97
P	SER119
P	ASN313
P	HOH605
P	HOH613
P	HOH657
R	HOH610

---

site_id	AC4
Number of Residues	4
Details	binding site for residue SO4 R 501

Chain	Residue
R	SER148
R	THR208
R	GLY209
R	ALA210

---

site_id	AC5
Number of Residues	4
Details	binding site for residue SO4 R 502

Chain	Residue
R	THR179
R	THR181
R	ARG231
R	NAD503

---

site_id	AC6
Number of Residues	13
Details	binding site for residue NAD R 503

Chain	Residue
R	GLY9
R	ARG10
R	ILE11
R	ASN31
R	ASP32
R	PRO33
R	ARG77
R	SER95
R	THR96
R	GLY97
R	SER119
R	ASN313
R	SO4502

---

site_id	AC7
Number of Residues	3
Details	binding site for residue SO4 S 501

Chain	Residue
S	THR208
S	GLY209
S	ALA210

---

site_id	AC8
Number of Residues	6
Details	binding site for residue SO4 S 502

Chain	Residue
S	THR179
S	THR181
S	ARG231
S	NAD503
S	HOH615
S	HOH624

---

site_id	AC9
Number of Residues	18
Details	binding site for residue NAD S 503

Chain	Residue
S	PHE8
S	GLY9
S	ARG10
S	ILE11
S	ASP32
S	PRO33
S	PHE34
S	ARG77
S	THR96
S	GLY97
S	SER119
S	ALA120
S	ASN313
S	SO4502
S	HOH620
S	HOH624
S	HOH625
S	HOH666

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
P	ALA147-LEU154

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	ACT_SITE: Nucleophile => ECO:0000255|PROSITE-ProRule:PRU10009

Chain	Residue	Details
P	CYS149
R	CYS149
S	CYS149

---

site_id	SWS_FT_FI2
Number of Residues	15
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	ARG10
R	ASN313
S	ARG10
S	ASP32
S	ARG77
S	SER119
S	ASN313
P	ASP32
P	ARG77
P	SER119
P	ASN313
R	ARG10
R	ASP32
R	ARG77
R	SER119

---

site_id	SWS_FT_FI3
Number of Residues	12
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P22513

Chain	Residue	Details
P	SER148
S	THR179
S	THR208
S	ARG231
P	THR179
P	THR208
P	ARG231
R	SER148
R	THR179
R	THR208
R	ARG231
S	SER148

---

site_id	SWS_FT_FI4
Number of Residues	3
Details	SITE: Activates thiol group during catalysis => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	HIS176
R	HIS176
S	HIS176

---

site_id	SWS_FT_FI5
Number of Residues	15
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	LYS2
R	LYS331
S	LYS2
S	LYS63
S	GLN257
S	LYS260
S	LYS331
P	LYS63
P	GLN257
P	LYS260
P	LYS331
R	LYS2
R	LYS63
R	GLN257
R	LYS260

---

site_id	SWS_FT_FI6
Number of Residues	21
Details	MOD_RES: Deamidated asparagine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	ASN6
R	ASN67
R	ASN146
R	ASN152
R	ASN222
R	ASN313
S	ASN6
S	ASN61
S	ASN67
S	ASN146
S	ASN152
P	ASN61
S	ASN222
S	ASN313
P	ASN67
P	ASN146
P	ASN152
P	ASN222
P	ASN313
R	ASN6
R	ASN61

---

site_id	SWS_FT_FI7
Number of Residues	3
Details	MOD_RES: Phosphotyrosine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	TYR39
R	TYR39
S	TYR39

---

site_id	SWS_FT_FI8
Number of Residues	9
Details	MOD_RES: N6-acetyllysine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	LYS58
P	LYS216
P	LYS251
R	LYS58
R	LYS216
R	LYS251
S	LYS58
S	LYS216
S	LYS251

---

site_id	SWS_FT_FI9
Number of Residues	24
Details	MOD_RES: Phosphothreonine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	THR72
R	THR150
R	THR174
R	THR179
R	THR181
R	THR208
R	THR226
R	THR234
S	THR72
S	THR150
S	THR174
P	THR150
S	THR179
S	THR181
S	THR208
S	THR226
S	THR234
P	THR174
P	THR179
P	THR181
P	THR208
P	THR226
P	THR234
R	THR72

---

site_id	SWS_FT_FI10
Number of Residues	18
Details	MOD_RES: Phosphoserine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	SER119
R	SER238
R	SER309
R	SER330
S	SER119
S	SER145
S	SER148
S	SER238
S	SER309
S	SER330
P	SER145
P	SER148
P	SER238
P	SER309
P	SER330
R	SER119
R	SER145
R	SER148

---

site_id	SWS_FT_FI11
Number of Residues	3
Details	MOD_RES: S-nitrosocysteine; in reversibly inhibited form => ECO:0000250|UniProtKB:P04797

Chain	Residue	Details
P	CYS149
R	CYS149
S	CYS149

---

site_id	SWS_FT_FI12
Number of Residues	6
Details	MOD_RES: N6-malonyllysine; alternate => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	LYS191
P	LYS212
R	LYS191
R	LYS212
S	LYS191
S	LYS212

---

site_id	SWS_FT_FI13
Number of Residues	3
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	LYS224
R	LYS224
S	LYS224

---

site_id	SWS_FT_FI14
Number of Residues	3
Details	MOD_RES: S-nitrosocysteine => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	CYS244
R	CYS244
S	CYS244

---

site_id	SWS_FT_FI15
Number of Residues	6
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0000250|UniProtKB:P04406

Chain	Residue	Details
P	LYS183
R	LYS183
S	LYS183

---