3D4P

Crystal structure of Lactate Dehydrogenase from Staphylococcus Aureus complexed with NAD and pyruvate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
A	0005737	cellular_component	cytoplasm
A	0006089	biological_process	lactate metabolic process
A	0006096	biological_process	glycolytic process
A	0016491	molecular_function	oxidoreductase activity
A	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
A	0019752	biological_process	carboxylic acid metabolic process
B	0003824	molecular_function	catalytic activity
B	0004459	molecular_function	L-lactate dehydrogenase (NAD+) activity
B	0005737	cellular_component	cytoplasm
B	0006089	biological_process	lactate metabolic process
B	0006096	biological_process	glycolytic process
B	0016491	molecular_function	oxidoreductase activity
B	0016616	molecular_function	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
B	0019752	biological_process	carboxylic acid metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	15
Details	BINDING SITE FOR RESIDUE NAD A 318

Chain	Residue
A	GLY15
A	THR123
A	ASN124
A	SER147
A	LEU151
A	HIS179
A	THR232
A	ALA16
A	ASP38
A	LEU39
A	CYS81
A	ALA82
A	GLY83
A	ALA84
A	ALA122

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PYR A 319

Chain	Residue
A	ASN124
A	LEU151
A	ARG155
A	HIS179
A	ALA222
A	THR232

---

site_id	AC3
Number of Residues	15
Details	BINDING SITE FOR RESIDUE NAD B 318

Chain	Residue
B	GLY15
B	ALA16
B	ASP38
B	LEU39
B	CYS81
B	ALA82
B	GLY83
B	ALA84
B	ALA122
B	THR123
B	ASN124
B	SER147
B	LEU151
B	HIS179
B	THR232

---

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PYR B 319

Chain	Residue
B	ASN124
B	LEU151
B	ARG155
B	HIS179
B	ALA222
B	THR232

---

Functional Information from PROSITE/UniProt

site_id	PS00064
Number of Residues	7
Details	L_LDH L-lactate dehydrogenase active site. IGEHGDT

Chain	Residue	Details
A	ILE176-THR182

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"MAY-2008","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase from Staphylococcus aureus complexed with NAD and pyruvate.","authors":["Schramm V.L.","Almo S.C.","Gutierrez J.A.","Ho M."]}},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate.","authors":["Ho M.-C.","Almo S.C.","Schramm V.L."]}},{"source":"PDB","id":"3D4P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3H3J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2008","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase from Staphylococcus aureus complexed with NAD and pyruvate.","authors":["Schramm V.L.","Almo S.C.","Gutierrez J.A.","Ho M."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate.","authors":["Ho M.-C.","Almo S.C.","Schramm V.L."]}},{"source":"PDB","id":"3D4P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3H3J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"MAY-2008","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase from Staphylococcus aureus complexed with NAD and pyruvate.","authors":["Schramm V.L.","Almo S.C.","Gutierrez J.A.","Ho M."]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate.","authors":["Ho M.-C.","Almo S.C.","Schramm V.L."]}},{"source":"PDB","id":"3D4P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3H3J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	14
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate.","authors":["Ho M.-C.","Almo S.C.","Schramm V.L."]}},{"source":"PDB","id":"3H3J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate.","authors":["Ho M.-C.","Almo S.C.","Schramm V.L."]}},{"source":"PDB","id":"3H3J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"MAY-2008","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase from Staphylococcus aureus complexed with NAD and pyruvate.","authors":["Schramm V.L.","Almo S.C.","Gutierrez J.A.","Ho M."]}},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"APR-2009","submissionDatabase":"PDB data bank","title":"Crystal structure of lactate dehydrogenase mutant (A85R) from staphylococcus aureus complexed with NAD and pyruvate.","authors":["Ho M.-C.","Almo S.C.","Schramm V.L."]}},{"source":"PDB","id":"3D4P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3H3J","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	2
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"HAMAP-Rule","id":"MF_00488","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
A	HIS179
A	ASP152

---

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

Chain	Residue	Details
B	HIS179
B	ASP152

---

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
A	HIS179
A	ARG155
A	ASP152

---

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1emd

Chain	Residue	Details
B	HIS179
B	ARG155
B	ASP152

---