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	0002376	biological_process	immune system process
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	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	0002376	biological_process	immune system process
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	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	0002376	biological_process	immune system process
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	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	0002376	biological_process	immune system process
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	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	20
Details	Motif: {"description":"[IL]-x-C-x-x-[DE] motif","evidences":[{"source":"PubMed","id":"25417112","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"25086035","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16239728","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16510976","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	20
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22513","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"PubMed","id":"16239728","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"16510976","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	20
Details	Modified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	28
Details	Modified residue: {"description":"Deamidated asparagine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	4
Details	Modified residue: {"description":"Methionine sulfoxide; in vitro","evidences":[{"source":"PubMed","id":"25086035","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	12
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"17081983","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	8
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	4
Details	Modified residue: {"description":"S-nitrosocysteine; in reversibly inhibited form","evidences":[{"source":"UniProtKB","id":"P04797","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	8
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18669648","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	8
Details	Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"PubMed","id":"21908771","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	4
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	4
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI24
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI25
Number of Residues	4
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"PubMed","id":"22771119","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25417112","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI26
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI27
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI28
Number of Residues	8
Details	Glycosylation: {"description":"(Microbial infection) N-beta-linked (GlcNAc) arginine","evidences":[{"source":"PubMed","id":"28522607","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI29
Number of Residues	8
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"PubMed","id":"28112733","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---