Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5LUC

Crystal structure of the D183N variant of human Alanine:Glyoxylate Aminotransferase major allele (AGT-Ma) at 1.8 Angstrom; internal aldimine with PLP in the active site

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004760	molecular_function	serine-pyruvate transaminase activity
A	0005515	molecular_function	protein binding
A	0005777	cellular_component	peroxisome
A	0005782	cellular_component	peroxisomal matrix
A	0005829	cellular_component	cytosol
A	0006563	biological_process	L-serine metabolic process
A	0007219	biological_process	Notch signaling pathway
A	0008453	molecular_function	alanine-glyoxylate transaminase activity
A	0008483	molecular_function	transaminase activity
A	0009436	biological_process	glyoxylate catabolic process
A	0016597	molecular_function	amino acid binding
A	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
A	0019448	biological_process	L-cysteine catabolic process
A	0030170	molecular_function	pyridoxal phosphate binding
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0042853	biological_process	L-alanine catabolic process
A	0043231	cellular_component	intracellular membrane-bounded organelle
A	0046487	biological_process	glyoxylate metabolic process
A	0046724	biological_process	oxalic acid secretion
B	0004760	molecular_function	serine-pyruvate transaminase activity
B	0005515	molecular_function	protein binding
B	0005777	cellular_component	peroxisome
B	0005782	cellular_component	peroxisomal matrix
B	0005829	cellular_component	cytosol
B	0006563	biological_process	L-serine metabolic process
B	0007219	biological_process	Notch signaling pathway
B	0008453	molecular_function	alanine-glyoxylate transaminase activity
B	0008483	molecular_function	transaminase activity
B	0009436	biological_process	glyoxylate catabolic process
B	0016597	molecular_function	amino acid binding
B	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
B	0019448	biological_process	L-cysteine catabolic process
B	0030170	molecular_function	pyridoxal phosphate binding
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0042853	biological_process	L-alanine catabolic process
B	0043231	cellular_component	intracellular membrane-bounded organelle
B	0046487	biological_process	glyoxylate metabolic process
B	0046724	biological_process	oxalic acid secretion
E	0004760	molecular_function	serine-pyruvate transaminase activity
E	0005515	molecular_function	protein binding
E	0005777	cellular_component	peroxisome
E	0005782	cellular_component	peroxisomal matrix
E	0005829	cellular_component	cytosol
E	0006563	biological_process	L-serine metabolic process
E	0007219	biological_process	Notch signaling pathway
E	0008453	molecular_function	alanine-glyoxylate transaminase activity
E	0008483	molecular_function	transaminase activity
E	0009436	biological_process	glyoxylate catabolic process
E	0016597	molecular_function	amino acid binding
E	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
E	0019448	biological_process	L-cysteine catabolic process
E	0030170	molecular_function	pyridoxal phosphate binding
E	0042802	molecular_function	identical protein binding
E	0042803	molecular_function	protein homodimerization activity
E	0042853	biological_process	L-alanine catabolic process
E	0043231	cellular_component	intracellular membrane-bounded organelle
E	0046487	biological_process	glyoxylate metabolic process
E	0046724	biological_process	oxalic acid secretion
G	0004760	molecular_function	serine-pyruvate transaminase activity
G	0005515	molecular_function	protein binding
G	0005777	cellular_component	peroxisome
G	0005782	cellular_component	peroxisomal matrix
G	0005829	cellular_component	cytosol
G	0006563	biological_process	L-serine metabolic process
G	0007219	biological_process	Notch signaling pathway
G	0008453	molecular_function	alanine-glyoxylate transaminase activity
G	0008483	molecular_function	transaminase activity
G	0009436	biological_process	glyoxylate catabolic process
G	0016597	molecular_function	amino acid binding
G	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
G	0019448	biological_process	L-cysteine catabolic process
G	0030170	molecular_function	pyridoxal phosphate binding
G	0042802	molecular_function	identical protein binding
G	0042803	molecular_function	protein homodimerization activity
G	0042853	biological_process	L-alanine catabolic process
G	0043231	cellular_component	intracellular membrane-bounded organelle
G	0046487	biological_process	glyoxylate metabolic process
G	0046724	biological_process	oxalic acid secretion
M	0004760	molecular_function	serine-pyruvate transaminase activity
M	0005515	molecular_function	protein binding
M	0005777	cellular_component	peroxisome
M	0005782	cellular_component	peroxisomal matrix
M	0005829	cellular_component	cytosol
M	0006563	biological_process	L-serine metabolic process
M	0007219	biological_process	Notch signaling pathway
M	0008453	molecular_function	alanine-glyoxylate transaminase activity
M	0008483	molecular_function	transaminase activity
M	0009436	biological_process	glyoxylate catabolic process
M	0016597	molecular_function	amino acid binding
M	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
M	0019448	biological_process	L-cysteine catabolic process
M	0030170	molecular_function	pyridoxal phosphate binding
M	0042802	molecular_function	identical protein binding
M	0042803	molecular_function	protein homodimerization activity
M	0042853	biological_process	L-alanine catabolic process
M	0043231	cellular_component	intracellular membrane-bounded organelle
M	0046487	biological_process	glyoxylate metabolic process
M	0046724	biological_process	oxalic acid secretion
N	0004760	molecular_function	serine-pyruvate transaminase activity
N	0005515	molecular_function	protein binding
N	0005777	cellular_component	peroxisome
N	0005782	cellular_component	peroxisomal matrix
N	0005829	cellular_component	cytosol
N	0006563	biological_process	L-serine metabolic process
N	0007219	biological_process	Notch signaling pathway
N	0008453	molecular_function	alanine-glyoxylate transaminase activity
N	0008483	molecular_function	transaminase activity
N	0009436	biological_process	glyoxylate catabolic process
N	0016597	molecular_function	amino acid binding
N	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
N	0019448	biological_process	L-cysteine catabolic process
N	0030170	molecular_function	pyridoxal phosphate binding
N	0042802	molecular_function	identical protein binding
N	0042803	molecular_function	protein homodimerization activity
N	0042853	biological_process	L-alanine catabolic process
N	0043231	cellular_component	intracellular membrane-bounded organelle
N	0046487	biological_process	glyoxylate metabolic process
N	0046724	biological_process	oxalic acid secretion
S	0004760	molecular_function	serine-pyruvate transaminase activity
S	0005515	molecular_function	protein binding
S	0005777	cellular_component	peroxisome
S	0005782	cellular_component	peroxisomal matrix
S	0005829	cellular_component	cytosol
S	0006563	biological_process	L-serine metabolic process
S	0007219	biological_process	Notch signaling pathway
S	0008453	molecular_function	alanine-glyoxylate transaminase activity
S	0008483	molecular_function	transaminase activity
S	0009436	biological_process	glyoxylate catabolic process
S	0016597	molecular_function	amino acid binding
S	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
S	0019448	biological_process	L-cysteine catabolic process
S	0030170	molecular_function	pyridoxal phosphate binding
S	0042802	molecular_function	identical protein binding
S	0042803	molecular_function	protein homodimerization activity
S	0042853	biological_process	L-alanine catabolic process
S	0043231	cellular_component	intracellular membrane-bounded organelle
S	0046487	biological_process	glyoxylate metabolic process
S	0046724	biological_process	oxalic acid secretion
T	0004760	molecular_function	serine-pyruvate transaminase activity
T	0005515	molecular_function	protein binding
T	0005777	cellular_component	peroxisome
T	0005782	cellular_component	peroxisomal matrix
T	0005829	cellular_component	cytosol
T	0006563	biological_process	L-serine metabolic process
T	0007219	biological_process	Notch signaling pathway
T	0008453	molecular_function	alanine-glyoxylate transaminase activity
T	0008483	molecular_function	transaminase activity
T	0009436	biological_process	glyoxylate catabolic process
T	0016597	molecular_function	amino acid binding
T	0019265	biological_process	glycine biosynthetic process, by transamination of glyoxylate
T	0019448	biological_process	L-cysteine catabolic process
T	0030170	molecular_function	pyridoxal phosphate binding
T	0042802	molecular_function	identical protein binding
T	0042803	molecular_function	protein homodimerization activity
T	0042853	biological_process	L-alanine catabolic process
T	0043231	cellular_component	intracellular membrane-bounded organelle
T	0046487	biological_process	glyoxylate metabolic process
T	0046724	biological_process	oxalic acid secretion

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	binding site for residue PLP A 401

Chain	Residue
A	SER81
A	GLN208
A	LYS209
B	TYR260
B	THR263
A	GLY82
A	HIS83
A	TRP108
A	GLY156
A	SER158
A	ASN183
A	VAL185
A	ALA186

site_id	AC2
Number of Residues	6
Details	binding site for residue BTB A 402

Chain	Residue
A	TRP246
A	ASN249
A	ASP254
A	GLN256
A	HOH568
A	HOH805

site_id	AC3
Number of Residues	6
Details	binding site for residue BTB B 402

Chain	Residue
B	TRP246
B	ASN249
B	ASP254
B	HOH545
B	HOH593
B	HOH727

site_id	AC4
Number of Residues	7
Details	binding site for residue BTB E 402

Chain	Residue
E	TRP246
E	ASN249
E	ASP254
E	GLN256
E	HOH609
E	HOH752
E	HOH816

site_id	AC5
Number of Residues	8
Details	binding site for residue BTB G 402

Chain	Residue
G	TRP246
G	ASN249
G	ASP254
G	GLN256
G	HOH547
G	HOH605
G	HOH777
G	HOH818

site_id	AC6
Number of Residues	7
Details	binding site for residue BTB M 402

Chain	Residue
M	TRP246
M	ASN249
M	ASP254
M	GLN256
M	HOH612
M	HOH619
M	HOH765

site_id	AC7
Number of Residues	8
Details	binding site for residue BTB N 402

Chain	Residue
N	TRP246
N	ASN249
N	ASP254
N	GLN256
N	HOH596
N	HOH738
N	HOH785
N	HOH790

site_id	AC8
Number of Residues	8
Details	binding site for residue BTB S 402

Chain	Residue
S	TRP246
S	ASN249
S	ASP254
S	GLN256
S	HOH540
S	HOH570
S	HOH773
S	HOH792

site_id	AC9
Number of Residues	7
Details	binding site for residue BTB T 402

Chain	Residue
T	TRP246
T	ASN249
T	ASP254
T	HOH614
T	HOH683
T	HOH720
T	HOH820

site_id	AD1
Number of Residues	19
Details	binding site for Di-peptide PLP B 401 and LYS B 209

Chain	Residue
A	TYR260
A	THR263
B	PRO28
B	SER31
B	SER81
B	GLY82
B	HIS83
B	TRP108
B	GLY156
B	SER158
B	ASN183
B	VAL185
B	ALA186
B	SER207
B	GLN208
B	ALA210
B	LEU211
B	ASN212
B	HOH687

site_id	AD2
Number of Residues	19
Details	binding site for Di-peptide PLP E 401 and LYS E 209

Chain	Residue
E	ALA186
E	SER207
E	GLN208
E	ALA210
E	LEU211
E	ASN212
E	HOH614
G	TYR260
G	THR263
E	PRO28
E	SER31
E	SER81
E	GLY82
E	HIS83
E	TRP108
E	GLY156
E	SER158
E	ASN183
E	VAL185

site_id	AD3
Number of Residues	19
Details	binding site for Di-peptide PLP G 401 and LYS G 209

Chain	Residue
E	TYR260
E	THR263
G	PRO28
G	SER31
G	SER81
G	GLY82
G	HIS83
G	TRP108
G	GLY156
G	SER158
G	ASN183
G	VAL185
G	ALA186
G	SER207
G	GLN208
G	ALA210
G	LEU211
G	ASN212
G	HOH676

site_id	AD4
Number of Residues	18
Details	binding site for Di-peptide PLP M 401 and LYS M 209

Chain	Residue
M	PRO28
M	SER31
M	SER81
M	GLY82
M	HIS83
M	TRP108
M	GLY156
M	SER158
M	ASN183
M	VAL185
M	ALA186
M	SER207
M	GLN208
M	ALA210
M	LEU211
M	ASN212
N	TYR260
N	THR263

site_id	AD5
Number of Residues	19
Details	binding site for Di-peptide PLP N 401 and LYS N 209

Chain	Residue
M	TYR260
M	THR263
N	PRO28
N	SER31
N	SER81
N	GLY82
N	HIS83
N	TRP108
N	GLY156
N	SER158
N	ASN183
N	VAL185
N	ALA186
N	SER207
N	GLN208
N	ALA210
N	LEU211
N	ASN212
N	HOH617

site_id	AD6
Number of Residues	19
Details	binding site for Di-peptide PLP S 401 and LYS S 209

Chain	Residue
S	PRO28
S	SER31
S	SER81
S	GLY82
S	HIS83
S	TRP108
S	GLY156
S	SER158
S	ASN183
S	VAL185
S	ALA186
S	SER207
S	GLN208
S	ALA210
S	LEU211
S	ASN212
S	HOH577
T	TYR260
T	THR263

site_id	AD7
Number of Residues	19
Details	binding site for Di-peptide PLP T 401 and LYS T 209

Chain	Residue
S	TYR260
S	THR263
T	PRO28
T	SER31
T	SER81
T	GLY82
T	HIS83
T	TRP108
T	GLY156
T	SER158
T	ASN183
T	VAL185
T	ALA186
T	SER207
T	GLN208
T	ALA210
T	LEU211
T	ASN212
T	HOH640

Functional Information from PROSITE/UniProt

site_id	PS00595
Number of Residues	21
Details	AA_TRANSFER_CLASS_5 Aminotransferases class-V pyridoxal-phosphate attachment site. IDILysGSQKalnappGtSlI

Chain	Residue	Details
A	ILE200-ILE220

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	BINDING:

Chain	Residue	Details
A	ARG360
B	ARG360
E	ARG360
G	ARG360
M	ARG360
N	ARG360
S	ARG360
T	ARG360

site_id	SWS_FT_FI2
Number of Residues	8
Details	MOD_RES: Phosphothreonine => ECO:0007744\|PubMed:24275569

Chain	Residue	Details
A	THR9
B	THR9
E	THR9
G	THR9
M	THR9
N	THR9
S	THR9
T	THR9

site_id	SWS_FT_FI3
Number of Residues	8
Details	MOD_RES: N6-(pyridoxal phosphate)lysine

Chain	Residue	Details
A	LYS209
B	LYS209
E	LYS209
G	LYS209
M	LYS209
N	LYS209
S	LYS209
T	LYS209

site_id	SWS_FT_FI4
Number of Residues	8
Details	MOD_RES: N6-succinyllysine; alternate => ECO:0000250\|UniProtKB:O35423

Chain	Residue	Details
A	LYS225
B	LYS225
E	LYS225
G	LYS225
M	LYS225
N	LYS225
S	LYS225
T	LYS225

site_id	SWS_FT_FI5
Number of Residues	16
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:O35423

Chain	Residue	Details
A	LYS234
M	LYS312
N	LYS234
N	LYS312
S	LYS234
S	LYS312
T	LYS234
T	LYS312
A	LYS312
B	LYS234
B	LYS312
E	LYS234
E	LYS312
G	LYS234
G	LYS312
M	LYS234

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)