6YEN

Crystal structure of AmpC from E. coli with Taniborbactam (VNRX-5133)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008800	molecular_function	beta-lactamase activity
A	0016787	molecular_function	hydrolase activity
A	0017001	biological_process	antibiotic catabolic process
A	0030288	cellular_component	outer membrane-bounded periplasmic space
A	0042597	cellular_component	periplasmic space
A	0046677	biological_process	response to antibiotic

Functional Information from PDB Data

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

Chain	Residue
A	SER64
A	GLY320
A	ASN346
A	HOH524
A	HOH711
A	GLN120
A	TYR150
A	ASN152
A	ASN289
A	LYS315
A	THR316
A	ALA318
A	THR319

---

site_id	AC2
Number of Residues	7
Details	binding site for residue MES A 402

Chain	Residue
A	GLN22
A	GLN23
A	LYS24
A	TYR40
A	THR42
A	GLN56
A	HOH506

---

site_id	AC3
Number of Residues	1
Details	binding site for residue PEG A 403

Chain	Residue
A	TRP93

---

site_id	AC4
Number of Residues	5
Details	binding site for residue EDO A 404

Chain	Residue
A	PRO5
A	LEU241
A	GLN249
A	HOH548
A	HOH671

---

site_id	AC5
Number of Residues	3
Details	binding site for residue EDO A 405

Chain	Residue
A	GLY36
A	LYS37
A	GLN235

---

site_id	AC6
Number of Residues	4
Details	binding site for residue EDO A 406

Chain	Residue
A	LYS50
A	GLY206
A	LYS207
A	ALA208

---

site_id	AC7
Number of Residues	11
Details	binding site for residue K9K A 407

Chain	Residue
A	THR97
A	GLN136
A	ASN137
A	PRO140
A	ALA141
A	TRP142
A	HOH509
A	HOH513
A	HOH593
A	HOH597
A	HOH658

---

site_id	AC8
Number of Residues	6
Details	binding site for residue ZN A 408

Chain	Residue
A	HIS13
A	HIS13
A	HIS13
A	CL410
A	CL410
A	CL410

---

site_id	AC9
Number of Residues	3
Details	binding site for residue ZN A 409

Chain	Residue
A	THR17
A	GLU21
A	HOH775

---

site_id	AD1
Number of Residues	6
Details	binding site for residue CL A 410

Chain	Residue
A	HIS13
A	HIS13
A	HIS13
A	ZN408
A	ZN408
A	ZN408

---

site_id	AD2
Number of Residues	2
Details	binding site for residue CL A 411

Chain	Residue
A	GLY320
A	HOH727

---

site_id	AD3
Number of Residues	4
Details	binding site for residue CL A 412

Chain	Residue
A	GLU171
A	GLN175
A	ILE189
A	ASN190

---

site_id	AD4
Number of Residues	4
Details	binding site for residue NA A 413

Chain	Residue
A	ASP217
A	HOH521
A	HOH646
A	HOH742

---

Functional Information from PROSITE/UniProt

site_id	PS00336
Number of Residues	8
Details	BETA_LACTAMASE_C Beta-lactamase class-C active site. FELGSVSK

Chain	Residue	Details
A	PHE60-LYS67

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Acyl-ester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU10102","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"11478888","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12005439","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16506777","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"35486701","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"6795623","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9819201","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"10504","lastPage":"10512","volume":"122","journal":"J. Am. Chem. Soc.","title":"Crystal Structures of Substrate and Inhibitor Complexes with AmpC Beta-Lactamase: Possible Implications for Substrate-Assisted Catalysis.","authors":["Patera A.","Blaszczak L.C.","Shoichet B.K."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001676x"}]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16506777","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"10504","lastPage":"10512","volume":"122","journal":"J. Am. Chem. Soc.","title":"Crystal Structures of Substrate and Inhibitor Complexes with AmpC Beta-Lactamase: Possible Implications for Substrate-Assisted Catalysis.","authors":["Patera A.","Blaszczak L.C.","Shoichet B.K."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001676x"}]}},{"source":"PDB","id":"1FCN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2FFY","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12005439","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12323371","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KVM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LL9","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16506777","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2FFY","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12005439","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12323371","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"16506777","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"2000","firstPage":"10504","lastPage":"10512","volume":"122","journal":"J. Am. Chem. Soc.","title":"Crystal Structures of Substrate and Inhibitor Complexes with AmpC Beta-Lactamase: Possible Implications for Substrate-Assisted Catalysis.","authors":["Patera A.","Blaszczak L.C.","Shoichet B.K."],"citationCrossReferences":[{"database":"DOI","id":"10.1021/ja001676x"}]}},{"source":"PDB","id":"1FCN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KVM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LL9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2FFY","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"12005439","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1KVM","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---