3L6B

X-ray crystal structure of human serine racemase in complex with malonate a potent inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
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	obsolete serine family amino acid metabolic process
A	0009410	biological_process	response to xenobiotic stimulus
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
A	1901986	biological_process	response to ketamine

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	BINDING SITE FOR RESIDUE PLP A 350

Chain	Residue
A	PHE55
A	GLU283
A	THR285
A	SER313
A	GLY314
A	MLI348
A	HOH355
A	HOH375
A	HOH403
A	HOH436
A	LYS56
A	ASN86
A	GLY185
A	GLY186
A	GLY187
A	GLY188
A	MET189
A	VAL240

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MN A 347

Chain	Residue
A	GLU210
A	ALA214
A	ASP216
A	HOH360
A	HOH376
A	HOH392

---

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE MLI A 348

Chain	Residue
A	LYS56
A	SER83
A	SER84
A	ASN86
A	HIS87
A	ARG135
A	GLY239
A	SER242
A	PLP350
A	HOH351
A	HOH373
A	HOH403

---

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	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"UniProtKB","id":"O59791","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7NBH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	9
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6ZSP","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7NBD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20106978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29277459","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3L6B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5X2L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBG","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"Q76EQ0","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"32039887","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"6SLH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6ZUJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBD","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20106978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3L6B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3L6R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"20106978","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3L6B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3L6R","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"7NBC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBG","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBH","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	1
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"PubMed","id":"20106978","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"29277459","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"35410329","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3L6B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5X2L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBF","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7NBG","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	1
Details	Modified residue: {"description":"S-nitrosocysteine","evidences":[{"source":"UniProtKB","id":"Q9QZX7","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---