Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5X2L

Crystal Structure of Human Serine Racemase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0003824	molecular_function	catalytic activity
A	0003941	molecular_function	L-serine ammonia-lyase activity
A	0005509	molecular_function	calcium ion binding
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006520	biological_process	amino acid metabolic process
A	0006563	biological_process	L-serine metabolic process
A	0008721	molecular_function	D-serine ammonia-lyase activity
A	0009069	biological_process	serine family amino acid metabolic process
A	0009410	biological_process	response to xenobiotic stimulus
A	0014070	biological_process	response to organic cyclic compound
A	0016594	molecular_function	glycine binding
A	0016829	molecular_function	lyase activity
A	0016853	molecular_function	isomerase activity
A	0018114	molecular_function	threonine racemase activity
A	0030165	molecular_function	PDZ domain binding
A	0030170	molecular_function	pyridoxal phosphate binding
A	0030378	molecular_function	serine racemase activity
A	0032496	biological_process	response to lipopolysaccharide
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0042866	biological_process	pyruvate biosynthetic process
A	0043025	cellular_component	neuronal cell body
A	0045177	cellular_component	apical part of cell
A	0046872	molecular_function	metal ion binding
A	0070178	biological_process	D-serine metabolic process
A	0070179	biological_process	D-serine biosynthetic process
B	0000287	molecular_function	magnesium ion binding
B	0003824	molecular_function	catalytic activity
B	0003941	molecular_function	L-serine ammonia-lyase activity
B	0005509	molecular_function	calcium ion binding
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006520	biological_process	amino acid metabolic process
B	0006563	biological_process	L-serine metabolic process
B	0008721	molecular_function	D-serine ammonia-lyase activity
B	0009069	biological_process	serine family amino acid metabolic process
B	0009410	biological_process	response to xenobiotic stimulus
B	0014070	biological_process	response to organic cyclic compound
B	0016594	molecular_function	glycine binding
B	0016829	molecular_function	lyase activity
B	0016853	molecular_function	isomerase activity
B	0018114	molecular_function	threonine racemase activity
B	0030165	molecular_function	PDZ domain binding
B	0030170	molecular_function	pyridoxal phosphate binding
B	0030378	molecular_function	serine racemase activity
B	0032496	biological_process	response to lipopolysaccharide
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0042866	biological_process	pyruvate biosynthetic process
B	0043025	cellular_component	neuronal cell body
B	0045177	cellular_component	apical part of cell
B	0046872	molecular_function	metal ion binding
B	0070178	biological_process	D-serine metabolic process
B	0070179	biological_process	D-serine biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	binding site for residue PLP A 401

Chain	Residue
A	PHE55
A	GLU283
A	THR285
A	SER313
A	HOH518
A	HOH533
A	HOH537
A	LYS56
A	ASN86
A	GLY185
A	GLY186
A	GLY187
A	GLY188
A	MET189
A	GLY239

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

Chain	Residue
A	GLU210
A	ALA214
A	ASP216
A	HOH528
A	HOH543
A	HOH552

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

Chain	Residue
B	GLU210
B	ALA214
B	ASP216
B	HOH531
B	HOH537
B	HOH553

site_id	AC4
Number of Residues	23
Details	binding site for Di-peptide PLP B 401 and LYS B 56

Chain	Residue
B	SER54
B	PHE55
B	ILE57
B	ARG58
B	GLY59
B	ALA60
B	ASN86
B	HIS87
B	ALA90
B	GLY185
B	GLY186
B	GLY187
B	GLY188
B	MET189
B	GLY239
B	GLU283
B	THR285
B	SER313
B	GLY314
B	HOH520
B	HOH530
B	HOH535
B	HOH556

Functional Information from PROSITE/UniProt

site_id	PS00165
Number of Residues	14
Details	DEHYDRATASE_SER_THR Serine/threonine dehydratases pyridoxal-phosphate attachment site. Elfqk.TGSFKIRGA

Chain	Residue	Details
A	GLU47-ALA60

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000250\|UniProtKB:O59791

Chain	Residue	Details
A	LYS56
A	SER84
B	LYS56
B	SER84

site_id	SWS_FT_FI2
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:7NBH

Chain	Residue	Details
A	GLU13
B	GLU13

site_id	SWS_FT_FI3
Number of Residues	18
Details	BINDING: BINDING => ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:6ZSP

Chain	Residue	Details
A	SER31
B	SER31
B	SER32
B	ILE33
B	LYS51
B	THR52
B	GLN89
B	TYR121
B	LYS279
B	ASN316
A	SER32
A	ILE33
A	LYS51
A	THR52
A	GLN89
A	TYR121
A	LYS279
A	ASN316

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:7NBC, ECO:0007744\|PDB:7NBF

Chain	Residue	Details
A	PRO69
B	PRO69

site_id	SWS_FT_FI5
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:7NBD

Chain	Residue	Details
A	THR81
B	THR81

site_id	SWS_FT_FI6
Number of Residues	14
Details	BINDING: BINDING => ECO:0000269\|PubMed:20106978, ECO:0000269\|PubMed:29277459, ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:3L6B, ECO:0007744\|PDB:5X2L, ECO:0007744\|PDB:7NBC, ECO:0007744\|PDB:7NBD, ECO:0007744\|PDB:7NBF, ECO:0007744\|PDB:7NBG

Chain	Residue	Details
A	ASN86
B	GLY186
B	GLY187
B	GLY188
B	MET189
B	SER313
A	GLY185
A	GLY186
A	GLY187
A	GLY188
A	MET189
A	SER313
B	ASN86
B	GLY185

site_id	SWS_FT_FI7
Number of Residues	2
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:Q76EQ0

Chain	Residue	Details
A	ASN154
B	ASN154

site_id	SWS_FT_FI8
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:32039887, ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:6SLH, ECO:0007744\|PDB:6ZUJ, ECO:0007744\|PDB:7NBD

Chain	Residue	Details
A	ASP178
B	ASP178

site_id	SWS_FT_FI9
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:20106978, ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:3L6B, ECO:0007744\|PDB:3L6R

Chain	Residue	Details
A	GLU210
B	GLU210

site_id	SWS_FT_FI10
Number of Residues	4
Details	BINDING: BINDING => ECO:0000269\|PubMed:20106978, ECO:0007744\|PDB:3L6B, ECO:0007744\|PDB:3L6R

Chain	Residue	Details
A	ALA214
A	ASP216
B	ALA214
B	ASP216

site_id	SWS_FT_FI11
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:7NBC, ECO:0007744\|PDB:7NBD, ECO:0007744\|PDB:7NBF, ECO:0007744\|PDB:7NBG, ECO:0007744\|PDB:7NBH

Chain	Residue	Details
A	ASN247
B	ASN247

site_id	SWS_FT_FI12
Number of Residues	2
Details	MOD_RES: N6-(pyridoxal phosphate)lysine => ECO:0000269\|PubMed:20106978, ECO:0000269\|PubMed:29277459, ECO:0000269\|PubMed:35410329, ECO:0007744\|PDB:3L6B, ECO:0007744\|PDB:5X2L, ECO:0007744\|PDB:7NBC, ECO:0007744\|PDB:7NBD, ECO:0007744\|PDB:7NBF, ECO:0007744\|PDB:7NBG

Chain	Residue	Details
A	LYS56
B	LYS56

site_id	SWS_FT_FI13
Number of Residues	2
Details	MOD_RES: S-nitrosocysteine => ECO:0000250\|UniProtKB:Q9QZX7

Chain	Residue	Details
A	CYS113
B	CYS113

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