5TSO

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 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	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	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	0061621	biological_process	canonical glycolysis
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	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	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	0061621	biological_process	canonical glycolysis
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	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	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	0061621	biological_process	canonical glycolysis
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	7
Details	binding site for residue SO4 P 501

Chain	Residue
P	SER148
P	THR151
P	THR208
P	GLY209
P	ALA210
P	HOH619
P	HOH698

---

site_id	AC2
Number of Residues	7
Details	binding site for residue SO4 P 502

Chain	Residue
P	ARG231
P	NAD503
P	HOH691
P	HOH748
P	HOH780
P	THR179
P	THR181

---

site_id	AC3
Number of Residues	35
Details	binding site for residue NAD P 503

Chain	Residue
P	ASN6
P	GLY7
P	PHE8
P	GLY9
P	ARG10
P	ILE11
P	ASN31
P	ASP32
P	PRO33
P	PHE34
P	ARG77
P	SER95
P	THR96
P	GLY97
P	SER119
P	ALA120
P	ALA180
P	ASN313
P	TYR317
P	SO4502
P	HOH630
P	HOH634
P	HOH645
P	HOH658
P	HOH681
P	HOH682
P	HOH684
P	HOH686
P	HOH694
P	HOH748
P	HOH752
P	HOH757
P	HOH760
P	HOH786
P	HOH796

---

site_id	AC4
Number of Residues	4
Details	binding site for residue SO4 P 504

Chain	Residue
P	ARG77
P	HOH609
P	HOH673
P	HOH715

---

site_id	AC5
Number of Residues	4
Details	binding site for residue SO4 P 505

Chain	Residue
P	SER263
P	LYS268
P	HIS288
P	HOH601

---

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 P 506

Chain	Residue
P	ASN301
P	ASP302
P	HIS303

---

site_id	AC7
Number of Residues	7
Details	binding site for residue GOL P 507

Chain	Residue
P	TYR46
P	LYS52
P	THR274
P	THR291
P	HOH647
P	HOH653
P	HOH669

---

site_id	AC8
Number of Residues	5
Details	binding site for residue PHN R 401

Chain	Residue
R	MET130
R	HIS134
R	LYS268
R	ILE270
S	GOL409

---

site_id	AC9
Number of Residues	9
Details	binding site for residue PHN R 402

Chain	Residue
R	VAL1
R	LYS24
R	ALA329
R	SER330
R	GOL408
R	HOH648
S	GLY265
S	PRO266
S	HOH680

---

site_id	AD1
Number of Residues	6
Details	binding site for residue SO4 R 403

Chain	Residue
R	SER148
R	THR151
R	THR208
R	GLY209
R	ALA210
R	HOH508

---

site_id	AD2
Number of Residues	6
Details	binding site for residue SO4 R 404

Chain	Residue
R	THR179
R	THR181
R	ARG231
R	NAD405
R	HOH522
R	HOH598

---

site_id	AD3
Number of Residues	33
Details	binding site for residue NAD R 405

Chain	Residue
R	ASN31
R	ASP32
R	PRO33
R	PHE34
R	ILE35
R	GLU76
R	ARG77
R	SER95
R	THR96
R	GLY97
R	SER119
R	ALA120
R	CYS149
R	ALA180
R	ASN313
R	TYR317
R	SO4404
R	HOH503
R	HOH513
R	HOH538
R	HOH579
R	HOH582
R	HOH592
R	HOH603
R	HOH613
R	HOH624
R	HOH640
R	ASN6
R	GLY7
R	PHE8
R	GLY9
R	ARG10
R	ILE11

---

site_id	AD4
Number of Residues	4
Details	binding site for residue SO4 R 406

Chain	Residue
R	GLN75
R	ARG77
R	HOH532
R	HOH555

---

site_id	AD5
Number of Residues	4
Details	binding site for residue SO4 R 407

Chain	Residue
R	ASN301
R	ASP302
R	HIS303
R	HOH510

---

site_id	AD6
Number of Residues	5
Details	binding site for residue GOL R 408

Chain	Residue
R	LYS24
R	PHN402
S	GLY265
S	PRO266
S	PHN401

---

site_id	AD7
Number of Residues	6
Details	binding site for residue GOL R 409

Chain	Residue
R	TYR46
R	THR274
R	PHE283
R	ASP286
R	THR291
R	HOH512

---

site_id	AD8
Number of Residues	9
Details	binding site for residue PHN S 401

Chain	Residue
R	GOL408
S	MET130
S	HIS134
S	PRO266
S	LYS268
S	ILE270
S	ASP323
S	HOH657
S	HOH798

---

site_id	AD9
Number of Residues	8
Details	binding site for residue PHN S 402

Chain	Residue
R	GLY265
R	PRO266
R	HOH628
S	VAL1
S	LYS24
S	ALA329
S	SER330
S	GOL409

---

site_id	AE1
Number of Residues	9
Details	binding site for residue SO4 S 403

Chain	Residue
S	SER148
S	THR208
S	GLY209
S	ALA210
S	HOH502
S	HOH520
S	HOH568
S	HOH599
S	HOH636

---

site_id	AE2
Number of Residues	8
Details	binding site for residue SO4 S 404

Chain	Residue
S	THR179
S	THR181
S	ARG231
S	NAD405
S	HOH611
S	HOH671
S	HOH678
S	HOH692

---

site_id	AE3
Number of Residues	36
Details	binding site for residue NAD S 405

Chain	Residue
S	ASN6
S	GLY7
S	PHE8
S	GLY9
S	ARG10
S	ILE11
S	ASN31
S	ASP32
S	PRO33
S	PHE34
S	GLU76
S	ARG77
S	SER95
S	THR96
S	GLY97
S	SER119
S	ALA120
S	CYS149
S	ALA180
S	PRO188
S	ASN313
S	TYR317
S	SO4404
S	HOH515
S	HOH556
S	HOH565
S	HOH571
S	HOH576
S	HOH578
S	HOH598
S	HOH620
S	HOH634
S	HOH668
S	HOH678
S	HOH686
S	HOH732

---

site_id	AE4
Number of Residues	4
Details	binding site for residue GOL S 406

Chain	Residue
S	ASN301
S	ASP302
S	HIS303
S	HOH609

---

site_id	AE5
Number of Residues	9
Details	binding site for residue GOL S 407

Chain	Residue
S	TYR46
S	LYS52
S	THR274
S	ASP282
S	THR291
S	HOH516
S	HOH564
S	HOH629
S	HOH667

---

site_id	AE6
Number of Residues	6
Details	binding site for residue GOL S 408

Chain	Residue
S	SER263
S	LYS268
S	HIS288
S	HOH557
S	HOH624
S	HOH730

---

site_id	AE7
Number of Residues	7
Details	binding site for residue GOL S 409

Chain	Residue
R	GLY265
R	PRO266
R	PHN401
S	LYS24
S	PHN402
S	HOH503
S	HOH505

---

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	432
Details	Region: {"description":"Interaction with WARS1","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	15
Details	Motif: {"description":"[IL]-x-C-x-x-[DE] motif","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	3
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PROSITE-ProRule","id":"PRU10009","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P22513","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	3
Details	Site: {"description":"Activates thiol group during catalysis","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	15
Details	Modified residue: {"description":"N6,N6-dimethyllysine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	21
Details	Modified residue: {"description":"Deamidated asparagine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	9
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	24
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	18
Details	Modified residue: {"description":"Phosphoserine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	3
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_FI14
Number of Residues	6
Details	Modified residue: {"description":"N6-malonyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	3
Details	Modified residue: {"description":"N6-acetyllysine; alternate","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	3
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	6
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)","evidences":[{"source":"UniProtKB","id":"P04406","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---