Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3GPD

TWINNING IN CRYSTALS OF HUMAN SKELETAL MUSCLE D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE

Functional Information from GO Data

Chain	GOid	namespace	contents
G	0000226	biological_process	microtubule cytoskeleton organization
G	0002376	biological_process	immune system process
G	0004365	molecular_function	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
G	0005515	molecular_function	protein binding
G	0005634	cellular_component	nucleus
G	0005737	cellular_component	cytoplasm
G	0005811	cellular_component	lipid droplet
G	0005829	cellular_component	cytosol
G	0005856	cellular_component	cytoskeleton
G	0005886	cellular_component	plasma membrane
G	0006006	biological_process	glucose metabolic process
G	0006096	biological_process	glycolytic process
G	0006417	biological_process	regulation of translation
G	0006915	biological_process	apoptotic process
G	0008017	molecular_function	microtubule binding
G	0015630	cellular_component	microtubule cytoskeleton
G	0016020	cellular_component	membrane
G	0016241	biological_process	regulation of macroautophagy
G	0016491	molecular_function	oxidoreductase activity
G	0016620	molecular_function	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor
G	0016740	molecular_function	transferase activity
G	0017148	biological_process	negative regulation of translation
G	0019828	molecular_function	aspartic-type endopeptidase inhibitor activity
G	0031982	cellular_component	vesicle
G	0032481	biological_process	positive regulation of type I interferon production
G	0035605	molecular_function	peptidyl-cysteine S-nitrosylase activity
G	0035606	biological_process	peptidyl-cysteine S-trans-nitrosylation
G	0042802	molecular_function	identical protein binding
G	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
G	0045087	biological_process	innate immune response
G	0048471	cellular_component	perinuclear region of cytoplasm
G	0050661	molecular_function	NADP binding
G	0050821	biological_process	protein stabilization
G	0051287	molecular_function	NAD binding
G	0051402	biological_process	neuron apoptotic process
G	0061621	biological_process	canonical glycolysis
G	0061760	biological_process	antifungal innate immune response
G	0061844	biological_process	antimicrobial humoral immune response mediated by antimicrobial peptide
G	0070062	cellular_component	extracellular exosome
G	0071346	biological_process	cellular response to type II interferon
G	0097452	cellular_component	GAIT complex
G	0097718	molecular_function	disordered domain specific binding
G	1901194	biological_process	negative regulation of formation of translation preinitiation complex
G	1990904	cellular_component	ribonucleoprotein complex
R	0000226	biological_process	microtubule cytoskeleton organization
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	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	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	0051287	molecular_function	NAD binding
R	0051402	biological_process	neuron apoptotic process
R	0061621	biological_process	canonical glycolysis
R	0061760	biological_process	antifungal innate immune response
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	1901194	biological_process	negative regulation of formation of translation preinitiation complex
R	1990904	cellular_component	ribonucleoprotein complex

Functional Information from PDB Data

site_id	ABR
Number of Residues	8
Details	RESIDUES INTERACTING WITH THE ADENINE BASE OF THE NAD COFACTOR IN THE RED SUBUNIT

Chain	Residue
R	ASP8
R	GLY9
R	ASN33
R	ASP34
R	PRO35
R	GLU78
R	ARG79
R	ASP80

site_id	AC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 R 338

Chain	Residue
R	THR181
R	THR183
R	NAD336

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 R 340

Chain	Residue
R	SER150
R	CYS151
R	THR210
R	GLY211

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 G 338

Chain	Residue
G	THR181
G	THR183
G	NAD336

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 G 340

Chain	Residue
G	SER150
G	CYS151
G	THR152
G	THR210
G	GLY211

site_id	AC5
Number of Residues	20
Details	BINDING SITE FOR RESIDUE NAD R 336

Chain	Residue
R	GLY9
R	GLY11
R	ARG12
R	ILE13
R	ASN33
R	ASP34
R	PRO35
R	PHE36
R	GLU78
R	ASP80
R	SER97
R	THR98
R	SER121
R	ALA122
R	CYS151
R	ILE180
R	ALA182
R	ASN315
R	GLU316
R	SO4338

site_id	AC6
Number of Residues	16
Details	BINDING SITE FOR RESIDUE NAD G 336

Chain	Residue
G	GLY9
G	GLY11
G	ARG12
G	ILE13
G	PRO35
G	ARG79
G	SER97
G	THR98
G	GLY99
G	PHE101
G	SER121
G	ALA122
G	CYS151
G	ALA182
G	ASN315
G	SO4338

site_id	APR
Number of Residues	2
Details	RESIDUES INTERACTING WITH THE PHOSPHATE OF THE ADENOSINE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT

Chain	Residue
R	GLY11
R	ARG12

site_id	ARR
Number of Residues	3
Details	RESIDUES INTERACTING WITH THE ADENOSINE RIBOSE OF THE NAD COFACTOR IN THE RED SUBUNIT

Chain	Residue
R	SER97
R	THR98
R	PHE36

site_id	IPR
Number of Residues	4
Details	RESIDUES INTERACTING WITH THE SUBSTRATE AND THE INORGANIC PHOSPHATE GROUPS RESPECTIVELY OF THE RED SUBUNIT

Chain	Residue
R	THR181
R	ALA182
R	THR183
R	ARG233

site_id	NBR
Number of Residues	4
Details	RESIDUES INTERACTING WITH THE NICOTINAMIDE BASE OF THE NAD COFACTOR IN THE RED SUBUNIT

Chain	Residue
R	CYS151
R	ILE180
R	ASN315
R	GLU316

site_id	NPR
Number of Residues	2
Details	RESIDUES INTERACTING WITH THE PHOSPHATE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT

Chain	Residue
R	ARG12
R	ILE13

site_id	NRR
Number of Residues	3
Details	RESIDUES INTERACTING WITH THE RIBOSE OF THE NICOTINAMIDE NUCLEOTIDE OF THE NAD COFACTOR IN THE RED SUBUNIT

Chain	Residue
R	ILE13
R	SER121
R	ALA122

site_id	SPR
Number of Residues	4
Details	RESIDUES INTERACTING WITH THE SUBSTRATE AND THE INORGANIC PHOSPHATE GROUPS RESPECTIVELY OF THE RED SUBUNIT

Chain	Residue
R	SER150
R	CYS151
R	THR152
R	THR210

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
R	ALA149-LEU156

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	292
Details	Region: {"description":"Interaction with WARS1","evidences":[{"source":"PubMed","id":"15628863","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	10
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_FI3
Number of Residues	2
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"25086035","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	10
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_FI5
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22513","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
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_FI7
Number of Residues	10
Details	Modified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	14
Details	Modified residue: {"description":"Deamidated asparagine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"15592455","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Modified residue: {"description":"Methionine sulfoxide; in vitro","evidences":[{"source":"PubMed","id":"25086035","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	2
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_FI13
Number of Residues	2
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_FI14
Number of Residues	4
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	2
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_FI16
Number of Residues	2
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_FI17
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	2
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_FI20
Number of Residues	4
Details	Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"PubMed","id":"21908771","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"19690332","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"PubMed","id":"19608861","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	2
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_FI24
Number of Residues	2
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"18183946","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"24275569","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	2
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_FI27
Number of Residues	2
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_FI28
Number of Residues	2
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	4
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_FI30
Number of Residues	4
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
R	CYS151
R	HIS178

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

Chain	Residue	Details
G	CYS151
G	HIS178

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)