1ZNQ

Crystal Structure of Human Liver GAPDH

Functional Information from GO Data

Chain	GOid	namespace	contents
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
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	0005515	molecular_function	protein binding
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	0010951	biological_process	negative regulation of endopeptidase activity
P	0015630	cellular_component	microtubule cytoskeleton
P	0016020	cellular_component	membrane
P	0016241	biological_process	regulation of macroautophagy
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	0031982	cellular_component	vesicle
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	0045087	biological_process	innate immune response
P	0048471	cellular_component	perinuclear region of cytoplasm
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	0070062	cellular_component	extracellular exosome
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
Q	0000226	biological_process	microtubule cytoskeleton organization
Q	0001819	biological_process	positive regulation of cytokine production
Q	0002376	biological_process	immune system process
Q	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
Q	0005515	molecular_function	protein binding
Q	0005634	cellular_component	nucleus
Q	0005737	cellular_component	cytoplasm
Q	0005811	cellular_component	lipid droplet
Q	0005829	cellular_component	cytosol
Q	0005856	cellular_component	cytoskeleton
Q	0005886	cellular_component	plasma membrane
Q	0006006	biological_process	glucose metabolic process
Q	0006096	biological_process	glycolytic process
Q	0006417	biological_process	regulation of translation
Q	0006915	biological_process	apoptotic process
Q	0008017	molecular_function	microtubule binding
Q	0010951	biological_process	negative regulation of endopeptidase activity
Q	0015630	cellular_component	microtubule cytoskeleton
Q	0016020	cellular_component	membrane
Q	0016241	biological_process	regulation of macroautophagy
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	0016740	molecular_function	transferase activity
Q	0017148	biological_process	negative regulation of translation
Q	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
Q	0031640	biological_process	killing of cells of another organism
Q	0031965	cellular_component	nuclear membrane
Q	0031982	cellular_component	vesicle
Q	0032481	biological_process	positive regulation of type I interferon production
Q	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
Q	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
Q	0042802	molecular_function	identical protein binding
Q	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
Q	0045087	biological_process	innate immune response
Q	0048471	cellular_component	perinuclear region of cytoplasm
Q	0050661	molecular_function	NADP binding
Q	0050821	biological_process	protein stabilization
Q	0050832	biological_process	defense response to fungus
Q	0051287	molecular_function	NAD binding
Q	0051402	biological_process	neuron apoptotic process
Q	0051873	biological_process	killing by host of symbiont cells
Q	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
Q	0070062	cellular_component	extracellular exosome
Q	0071346	biological_process	cellular response to type II interferon
Q	0097452	cellular_component	GAIT complex
Q	0097718	molecular_function	disordered domain specific binding
Q	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	0005515	molecular_function	protein binding
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	0010951	biological_process	negative regulation of endopeptidase activity
R	0015630	cellular_component	microtubule cytoskeleton
R	0016020	cellular_component	membrane
R	0016241	biological_process	regulation of macroautophagy
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	0031982	cellular_component	vesicle
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	0045087	biological_process	innate immune response
R	0048471	cellular_component	perinuclear region of cytoplasm
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	0070062	cellular_component	extracellular exosome
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

Functional Information from PDB Data

site_id	AC1
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD O 1001

Chain	Residue
O	ASN9
O	PHE37
O	ILE38
O	ARG80
O	SER98
O	THR99
O	GLY100
O	PHE102
O	SER122
O	ALA123
O	CYS152
O	GLY10
O	ASN316
O	HOH1010
O	PHE11
O	GLY12
O	ARG13
O	ILE14
O	ASN34
O	ASP35
O	PRO36

---

site_id	AC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD P 1002

Chain	Residue
P	ASN9
P	GLY10
P	PHE11
P	GLY12
P	ARG13
P	ILE14
P	ASP35
P	PRO36
P	PHE37
P	ILE38
P	ARG80
P	SER98
P	THR99
P	GLY100
P	SER122
P	ALA123
P	CYS152
P	ASN316
P	GLU317
P	TYR320
P	HOH1009
P	HOH1033

---

site_id	AC3
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD R 1003

Chain	Residue
R	ASN9
R	GLY10
R	PHE11
R	GLY12
R	ARG13
R	ILE14
R	ASP35
R	PRO36
R	PHE37
R	ILE38
R	ARG80
R	SER98
R	THR99
R	GLY100
R	SER122
R	ALA123
R	CYS152
R	ALA183
R	ASN316
R	TYR320
R	HOH1006
R	HOH1020

---

site_id	AC4
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD Q 1004

Chain	Residue
Q	ASN9
Q	GLY10
Q	PHE11
Q	GLY12
Q	ARG13
Q	ILE14
Q	ASP35
Q	PRO36
Q	PHE37
Q	ILE38
Q	ARG80
Q	SER98
Q	THR99
Q	GLY100
Q	PHE102
Q	SER122
Q	ALA123
Q	CYS152
Q	ASN316
Q	GLU317
Q	TYR320

---

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

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
O	HIS179
O	CYS152

---

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
P	HIS179
P	CYS152

---

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
R	HIS179
R	CYS152

---

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1szj

Chain	Residue	Details
Q	HIS179
Q	CYS152

---