4WNI

Crystal structure of the T229K mutant of human GAPDH at 2.3 angstroems resolution

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000226	biological_process	microtubule cytoskeleton organization
A	0001819	biological_process	positive regulation of cytokine production
A	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005737	cellular_component	cytoplasm
A	0005811	cellular_component	lipid droplet
A	0005829	cellular_component	cytosol
A	0005856	cellular_component	cytoskeleton
A	0005886	cellular_component	plasma membrane
A	0006006	biological_process	glucose metabolic process
A	0006096	biological_process	glycolytic process
A	0006417	biological_process	regulation of translation
A	0006915	biological_process	apoptotic process
A	0008017	molecular_function	microtubule binding
A	0010951	biological_process	negative regulation of endopeptidase activity
A	0015630	cellular_component	microtubule cytoskeleton
A	0016020	cellular_component	membrane
A	0016241	biological_process	regulation of macroautophagy
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	0016740	molecular_function	transferase activity
A	0017148	biological_process	negative regulation of translation
A	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
A	0031640	biological_process	killing of cells of another organism
A	0031965	cellular_component	nuclear membrane
A	0031982	cellular_component	vesicle
A	0032481	biological_process	positive regulation of type I interferon production
A	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
A	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
A	0042802	molecular_function	identical protein binding
A	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
A	0043231	cellular_component	intracellular membrane-bounded organelle
A	0045087	biological_process	innate immune response
A	0048471	cellular_component	perinuclear region of cytoplasm
A	0050661	molecular_function	NADP binding
A	0050821	biological_process	protein stabilization
A	0050832	biological_process	defense response to fungus
A	0051287	molecular_function	NAD binding
A	0051402	biological_process	neuron apoptotic process
A	0051873	biological_process	killing by host of symbiont cells
A	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
A	0070062	cellular_component	extracellular exosome
A	0071346	biological_process	cellular response to type II interferon
A	0097452	cellular_component	GAIT complex
A	0097718	molecular_function	disordered domain specific binding
A	1990904	cellular_component	ribonucleoprotein complex
B	0000226	biological_process	microtubule cytoskeleton organization
B	0001819	biological_process	positive regulation of cytokine production
B	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005737	cellular_component	cytoplasm
B	0005811	cellular_component	lipid droplet
B	0005829	cellular_component	cytosol
B	0005856	cellular_component	cytoskeleton
B	0005886	cellular_component	plasma membrane
B	0006006	biological_process	glucose metabolic process
B	0006096	biological_process	glycolytic process
B	0006417	biological_process	regulation of translation
B	0006915	biological_process	apoptotic process
B	0008017	molecular_function	microtubule binding
B	0010951	biological_process	negative regulation of endopeptidase activity
B	0015630	cellular_component	microtubule cytoskeleton
B	0016020	cellular_component	membrane
B	0016241	biological_process	regulation of macroautophagy
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	0016740	molecular_function	transferase activity
B	0017148	biological_process	negative regulation of translation
B	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
B	0031640	biological_process	killing of cells of another organism
B	0031965	cellular_component	nuclear membrane
B	0031982	cellular_component	vesicle
B	0032481	biological_process	positive regulation of type I interferon production
B	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
B	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
B	0042802	molecular_function	identical protein binding
B	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
B	0043231	cellular_component	intracellular membrane-bounded organelle
B	0045087	biological_process	innate immune response
B	0048471	cellular_component	perinuclear region of cytoplasm
B	0050661	molecular_function	NADP binding
B	0050821	biological_process	protein stabilization
B	0050832	biological_process	defense response to fungus
B	0051287	molecular_function	NAD binding
B	0051402	biological_process	neuron apoptotic process
B	0051873	biological_process	killing by host of symbiont cells
B	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
B	0070062	cellular_component	extracellular exosome
B	0071346	biological_process	cellular response to type II interferon
B	0097452	cellular_component	GAIT complex
B	0097718	molecular_function	disordered domain specific binding
B	1990904	cellular_component	ribonucleoprotein complex
C	0000226	biological_process	microtubule cytoskeleton organization
C	0001819	biological_process	positive regulation of cytokine production
C	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005737	cellular_component	cytoplasm
C	0005811	cellular_component	lipid droplet
C	0005829	cellular_component	cytosol
C	0005856	cellular_component	cytoskeleton
C	0005886	cellular_component	plasma membrane
C	0006006	biological_process	glucose metabolic process
C	0006096	biological_process	glycolytic process
C	0006417	biological_process	regulation of translation
C	0006915	biological_process	apoptotic process
C	0008017	molecular_function	microtubule binding
C	0010951	biological_process	negative regulation of endopeptidase activity
C	0015630	cellular_component	microtubule cytoskeleton
C	0016020	cellular_component	membrane
C	0016241	biological_process	regulation of macroautophagy
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	0016740	molecular_function	transferase activity
C	0017148	biological_process	negative regulation of translation
C	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
C	0031640	biological_process	killing of cells of another organism
C	0031965	cellular_component	nuclear membrane
C	0031982	cellular_component	vesicle
C	0032481	biological_process	positive regulation of type I interferon production
C	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
C	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
C	0042802	molecular_function	identical protein binding
C	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
C	0043231	cellular_component	intracellular membrane-bounded organelle
C	0045087	biological_process	innate immune response
C	0048471	cellular_component	perinuclear region of cytoplasm
C	0050661	molecular_function	NADP binding
C	0050821	biological_process	protein stabilization
C	0050832	biological_process	defense response to fungus
C	0051287	molecular_function	NAD binding
C	0051402	biological_process	neuron apoptotic process
C	0051873	biological_process	killing by host of symbiont cells
C	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
C	0070062	cellular_component	extracellular exosome
C	0071346	biological_process	cellular response to type II interferon
C	0097452	cellular_component	GAIT complex
C	0097718	molecular_function	disordered domain specific binding
C	1990904	cellular_component	ribonucleoprotein complex
O	0000226	biological_process	microtubule cytoskeleton organization
O	0001819	biological_process	positive regulation of cytokine production
O	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
O	0005515	molecular_function	protein binding
O	0005634	cellular_component	nucleus
O	0005737	cellular_component	cytoplasm
O	0005811	cellular_component	lipid droplet
O	0005829	cellular_component	cytosol
O	0005856	cellular_component	cytoskeleton
O	0005886	cellular_component	plasma membrane
O	0006006	biological_process	glucose metabolic process
O	0006096	biological_process	glycolytic process
O	0006417	biological_process	regulation of translation
O	0006915	biological_process	apoptotic process
O	0008017	molecular_function	microtubule binding
O	0010951	biological_process	negative regulation of endopeptidase activity
O	0015630	cellular_component	microtubule cytoskeleton
O	0016020	cellular_component	membrane
O	0016241	biological_process	regulation of macroautophagy
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	0016740	molecular_function	transferase activity
O	0017148	biological_process	negative regulation of translation
O	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
O	0031640	biological_process	killing of cells of another organism
O	0031965	cellular_component	nuclear membrane
O	0031982	cellular_component	vesicle
O	0032481	biological_process	positive regulation of type I interferon production
O	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
O	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
O	0042802	molecular_function	identical protein binding
O	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
O	0043231	cellular_component	intracellular membrane-bounded organelle
O	0045087	biological_process	innate immune response
O	0048471	cellular_component	perinuclear region of cytoplasm
O	0050661	molecular_function	NADP binding
O	0050821	biological_process	protein stabilization
O	0050832	biological_process	defense response to fungus
O	0051287	molecular_function	NAD binding
O	0051402	biological_process	neuron apoptotic process
O	0051873	biological_process	killing by host of symbiont cells
O	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
O	0070062	cellular_component	extracellular exosome
O	0071346	biological_process	cellular response to type II interferon
O	0097452	cellular_component	GAIT complex
O	0097718	molecular_function	disordered domain specific binding
O	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	28
Details	binding site for residue NAD O 401

Chain	Residue
O	ASN9
O	ARG80
O	SER98
O	THR99
O	GLY100
O	PHE102
O	SER122
O	ALA123
O	CYS152
O	ALA183
O	ASN316
O	GLY10
O	TYR320
O	HOH543
O	HOH553
O	HOH568
O	HOH569
O	HOH629
O	HOH676
O	HOH678
O	HOH729
O	GLY12
O	ARG13
O	ILE14
O	ASN34
O	ASP35
O	PRO36
O	PHE37

---

site_id	AC2
Number of Residues	6
Details	binding site for residue ZN O 402

Chain	Residue
B	GLU335
B	HOH501
B	HOH505
O	HIS330
O	HOH504
O	HOH509

---

site_id	AC3
Number of Residues	3
Details	binding site for residue ZN O 403

Chain	Residue
A	GLU138
A	HIS330
O	GLU63

---

site_id	AC4
Number of Residues	27
Details	binding site for residue NAD A 401

Chain	Residue
A	ASN9
A	GLY10
A	GLY12
A	ARG13
A	ILE14
A	ASN34
A	ASP35
A	PRO36
A	PHE37
A	ARG80
A	SER98
A	THR99
A	GLY100
A	PHE102
A	SER122
A	ALA123
A	CYS152
A	ALA183
A	ASN316
A	HOH542
A	HOH544
A	HOH545
A	HOH552
A	HOH637
A	HOH695
A	HOH732
A	HOH733

---

site_id	AC5
Number of Residues	24
Details	binding site for residue NAD B 401

Chain	Residue
B	ASN9
B	GLY10
B	PHE11
B	GLY12
B	ARG13
B	ILE14
B	ASN34
B	ASP35
B	PRO36
B	PHE37
B	ARG80
B	SER98
B	THR99
B	GLY100
B	PHE102
B	SER122
B	ALA123
B	CYS152
B	ASN316
B	HOH540
B	HOH571
B	HOH629
B	HOH643
B	HOH644

---

site_id	AC6
Number of Residues	4
Details	binding site for residue ZN B 402

Chain	Residue
A	HIS306
A	HOH518
B	GLU106
B	ASP127

---

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
O	ALA150-LEU157

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Nucleophile => ECO:0000269|PubMed:25086035

Chain	Residue	Details
O	CYS152
A	CYS152
B	CYS152
C	CYS152

---

site_id	SWS_FT_FI2
Number of Residues	20
Details	BINDING: BINDING => ECO:0000269|PubMed:16239728, ECO:0000269|PubMed:16510976

Chain	Residue	Details
O	ASN316
A	ARG13
A	ASP35
A	ARG80
A	SER122
A	ASN316
B	ARG13
B	ASP35
B	ARG80
B	SER122
B	ASN316
C	ARG13
C	ASP35
C	ARG80
C	SER122
C	ASN316
O	ARG13
O	ASP35
O	ARG80
O	SER122

---

site_id	SWS_FT_FI3
Number of Residues	16
Details	BINDING: BINDING => ECO:0000250|UniProtKB:P22513

Chain	Residue	Details
C	SER151
C	THR182
C	THR211
C	ARG234
A	SER151
A	THR182
O	SER151
O	THR182
O	THR211
O	ARG234
A	THR211
A	ARG234
B	SER151
B	THR182
B	THR211
B	ARG234

---

site_id	SWS_FT_FI4
Number of Residues	4
Details	SITE: Activates thiol group during catalysis => ECO:0000305|PubMed:16239728, ECO:0000305|PubMed:16510976

Chain	Residue	Details
A	HIS179
O	HIS179
B	HIS179
C	HIS179

---

site_id	SWS_FT_FI5
Number of Residues	20
Details	MOD_RES: N6,N6-dimethyllysine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
A	LYS263
A	LYS334
B	LYS5
B	LYS66
B	LYS260
B	LYS263
B	LYS334
C	LYS5
C	LYS66
C	LYS260
C	LYS263
C	LYS334
O	LYS260
O	LYS263
O	LYS5
O	LYS66
O	LYS334
A	LYS5
A	LYS66
A	LYS260

---

site_id	SWS_FT_FI6
Number of Residues	28
Details	MOD_RES: Deamidated asparagine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
O	ASN155
O	ASN225
O	ASN316
A	ASN9
A	ASN64
A	ASN70
A	ASN149
A	ASN155
A	ASN225
A	ASN316
B	ASN9
B	ASN64
B	ASN70
B	ASN149
B	ASN155
B	ASN225
B	ASN316
C	ASN9
C	ASN64
C	ASN70
C	ASN149
C	ASN155
C	ASN225
C	ASN316
O	ASN9
O	ASN64
O	ASN70
O	ASN149

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Phosphotyrosine => ECO:0007744|PubMed:15592455

Chain	Residue	Details
A	TYR42
B	TYR42
C	TYR42
O	TYR42

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	MOD_RES: Methionine sulfoxide; in vitro => ECO:0000305|PubMed:25086035

Chain	Residue	Details
A	MET46
B	MET46
C	MET46
O	MET46

---

site_id	SWS_FT_FI9
Number of Residues	12
Details	MOD_RES: N6-acetyllysine => ECO:0007744|PubMed:19608861

Chain	Residue	Details
A	LYS219
A	LYS254
B	LYS61
B	LYS219
B	LYS254
C	LYS61
C	LYS219
C	LYS254
O	LYS61
O	LYS219
O	LYS254
A	LYS61

---

site_id	SWS_FT_FI10
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:20068231

Chain	Residue	Details
A	THR75
O	THR75
B	THR75
C	THR75

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:17081983, ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:21406692, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER83
B	SER83
C	SER83
O	SER83

---

site_id	SWS_FT_FI12
Number of Residues	8
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
B	SER122
B	SER148
C	SER122
C	SER148
O	SER148
A	SER122
A	SER148
O	SER122

---

site_id	SWS_FT_FI13
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:23186163

Chain	Residue	Details
A	SER151
B	SER151
C	SER151
O	SER151

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine; in reversibly inhibited form => ECO:0000250|UniProtKB:P04797

Chain	Residue	Details
A	CYS152
O	CYS152
B	CYS152
C	CYS152

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	THR153
A	THR153
B	THR153
C	THR153

---

site_id	SWS_FT_FI16
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
B	THR177
B	THR182
C	THR177
C	THR182
O	THR177
A	THR177
A	THR182
O	THR182

---

site_id	SWS_FT_FI17
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:18669648, ECO:0007744|PubMed:19690332, ECO:0007744|PubMed:20068231, ECO:0007744|PubMed:24275569

Chain	Residue	Details
O	THR184
A	THR184
B	THR184
C	THR184

---

site_id	SWS_FT_FI18
Number of Residues	8
Details	MOD_RES: N6-malonyllysine; alternate => ECO:0000269|PubMed:21908771

Chain	Residue	Details
O	LYS194
O	LYS215
A	LYS194
A	LYS215
B	LYS194
B	LYS215
C	LYS194
C	LYS215

---

site_id	SWS_FT_FI19
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0007744|PubMed:19690332

Chain	Residue	Details
O	THR211
A	THR211
B	THR211
C	THR211

---

site_id	SWS_FT_FI20
Number of Residues	4
Details	MOD_RES: N6-acetyllysine; alternate => ECO:0007744|PubMed:19608861

Chain	Residue	Details
O	LYS227
A	LYS227
B	LYS227
C	LYS227

---

site_id	SWS_FT_FI21
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	LYS229
A	LYS229
B	LYS229
C	LYS229

---

site_id	SWS_FT_FI22
Number of Residues	4
Details	MOD_RES: Phosphothreonine => ECO:0000269|PubMed:18183946

Chain	Residue	Details
O	THR237
A	THR237
B	THR237
C	THR237

---

site_id	SWS_FT_FI23
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:24275569

Chain	Residue	Details
O	SER241
A	SER241
B	SER241
C	SER241

---

site_id	SWS_FT_FI24
Number of Residues	4
Details	MOD_RES: S-nitrosocysteine => ECO:0000269|PubMed:22771119, ECO:0000269|PubMed:25417112

Chain	Residue	Details
O	CYS247
A	CYS247
B	CYS247
C	CYS247

---

site_id	SWS_FT_FI25
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0000269|PubMed:18183946, ECO:0007744|PubMed:19690332

Chain	Residue	Details
O	SER312
A	SER312
B	SER312
C	SER312

---

site_id	SWS_FT_FI26
Number of Residues	4
Details	MOD_RES: Phosphoserine => ECO:0007744|PubMed:23186163

Chain	Residue	Details
O	SER333
A	SER333
B	SER333
C	SER333

---

site_id	SWS_FT_FI27
Number of Residues	8
Details	CARBOHYD: (Microbial infection) N-beta-linked (GlcNAc) arginine => ECO:0000269|PubMed:28522607

Chain	Residue	Details
B	ARG197
B	ARG200
C	ARG197
C	ARG200
O	ARG197
O	ARG200
A	ARG197
A	ARG200

---

site_id	SWS_FT_FI28
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2) => ECO:0007744|PubMed:28112733

Chain	Residue	Details
B	LYS186
C	LYS186
O	LYS186
A	LYS186

---