Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6ZRJ

Crystal structure of class D Beta-lactamase OXA-48 in complex with ertapenem

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008658	molecular_function	penicillin binding
A	0008800	molecular_function	beta-lactamase activity
A	0017001	biological_process	antibiotic catabolic process
B	0008658	molecular_function	penicillin binding
B	0008800	molecular_function	beta-lactamase activity
B	0017001	biological_process	antibiotic catabolic process
C	0008658	molecular_function	penicillin binding
C	0008800	molecular_function	beta-lactamase activity
C	0017001	biological_process	antibiotic catabolic process
D	0008658	molecular_function	penicillin binding
D	0008800	molecular_function	beta-lactamase activity
D	0017001	biological_process	antibiotic catabolic process
E	0008658	molecular_function	penicillin binding
E	0008800	molecular_function	beta-lactamase activity
E	0017001	biological_process	antibiotic catabolic process
F	0008658	molecular_function	penicillin binding
F	0008800	molecular_function	beta-lactamase activity
F	0017001	biological_process	antibiotic catabolic process
G	0008658	molecular_function	penicillin binding
G	0008800	molecular_function	beta-lactamase activity
G	0017001	biological_process	antibiotic catabolic process
H	0008658	molecular_function	penicillin binding
H	0008800	molecular_function	beta-lactamase activity
H	0017001	biological_process	antibiotic catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	16
Details	binding site for residue 2RG A 501

Chain	Residue
A	ALA69
A	TYR211
A	LEU247
A	ARG250
A	HOH605
A	HOH624
A	HOH662
A	HOH757
A	SER70
A	KCX73
A	ILE102
A	THR104
A	TYR117
A	VAL120
A	LEU158
A	GLY210

site_id	AC2
Number of Residues	5
Details	binding site for residue EDO A 502

Chain	Residue
A	LEU81
A	SER184
A	ARG186
A	SER187
A	HOH621

site_id	AC3
Number of Residues	5
Details	binding site for residue EDO A 503

Chain	Residue
A	ASP229
A	ASP230
A	HOH687
A	HOH716
B	ASN110

site_id	AC4
Number of Residues	3
Details	binding site for residue CL A 504

Chain	Residue
A	ARG206
B	ARG206
B	HOH771

site_id	AC5
Number of Residues	13
Details	binding site for residue 2RG B 501

Chain	Residue
B	ALA69
B	SER70
B	THR104
B	TYR117
B	VAL120
B	LEU158
B	GLY210
B	TYR211
B	ARG250
B	HOH615
B	HOH624
B	HOH654
B	HOH696

site_id	AC6
Number of Residues	7
Details	binding site for residue EDO B 502

Chain	Residue
A	LYS116
B	ASN200
B	GLU227
B	LEU228
B	ASP229
B	HOH622
B	HOH725

site_id	AC7
Number of Residues	6
Details	binding site for residue EDO B 503

Chain	Residue
B	SER40
B	ASP240
B	MET241
B	PRO242
B	HOH613
B	HOH639

site_id	AC8
Number of Residues	5
Details	binding site for residue EDO B 504

Chain	Residue
B	ASP82
B	SER184
B	ARG186
B	SER187
B	HOH794

site_id	AC9
Number of Residues	2
Details	binding site for residue EDO B 505

Chain	Residue
A	ASN110
B	ASP229

site_id	AD1
Number of Residues	7
Details	binding site for residue EDO B 506

Chain	Residue
B	GLN64
B	ALA65
B	PHE66
B	HOH608
B	HOH635
B	HOH653
B	HOH715

site_id	AD2
Number of Residues	7
Details	binding site for residue EDO B 507

Chain	Residue
A	HIS90
A	HOH602
A	HOH674
B	TYR177
B	GLU227
B	VAL232
B	HOH607

site_id	AD3
Number of Residues	7
Details	binding site for residue EDO C 502

Chain	Residue
C	TYR177
C	GLU227
C	VAL232
C	HOH635
C	HOH668
D	HIS90
D	HOH505

site_id	AD4
Number of Residues	5
Details	binding site for residue EDO C 503

Chain	Residue
C	ASN200
C	ASP229
C	HOH669
C	HOH686
D	LYS116

site_id	AD5
Number of Residues	8
Details	binding site for residue PGE D 401

Chain	Residue
C	ASN110
C	ILE112
C	LYS116
D	ASN200
D	ILE204
D	LEU228
D	ASP229
D	HOH574

site_id	AD6
Number of Residues	5
Details	binding site for residue EDO D 403

Chain	Residue
D	ASP229
D	HOH526
C	ASP108
C	ASN110
C	HOH620

site_id	AD7
Number of Residues	5
Details	binding site for residue EDO F 502

Chain	Residue
F	LEU81
F	SER184
F	ARG186
F	SER187
F	HOH673

site_id	AD8
Number of Residues	7
Details	binding site for residue EDO G 502

Chain	Residue
G	TYR177
G	GLU227
G	VAL232
G	HOH610
G	HOH648
H	HIS90
H	HOH618

site_id	AD9
Number of Residues	7
Details	binding site for residue EDO H 502

Chain	Residue
G	HIS90
G	HOH625
H	TYR177
H	GLU227
H	VAL232
H	HOH608
H	HOH670

site_id	AE1
Number of Residues	3
Details	binding site for residue EDO H 503

Chain	Residue
H	SER184
H	ARG186
H	SER187

site_id	AE2
Number of Residues	19
Details	binding site for Di-peptide 8FB C 501 and SER C 70

Chain	Residue
C	PRO68
C	ALA69
C	THR71
C	PHE72
C	KCX73
C	THR104
C	VAL120
C	LEU158
C	LYS208
C	THR209
C	GLY210
C	TYR211
C	LEU247
C	ARG250
C	HOH605
C	HOH651
C	HOH683
C	HOH707
C	HOH719

site_id	AE3
Number of Residues	17
Details	binding site for Di-peptide 8FB D 402 and SER D 70

Chain	Residue
D	PRO68
D	ALA69
D	THR71
D	PHE72
D	KCX73
D	THR104
D	TYR117
D	VAL120
D	LEU158
D	LYS208
D	THR209
D	GLY210
D	TYR211
D	LEU247
D	ARG250
D	HOH518
D	HOH540

site_id	AE4
Number of Residues	16
Details	binding site for Di-peptide 8FB E 501 and SER E 70

Chain	Residue
E	PRO68
E	ALA69
E	THR71
E	PHE72
E	KCX73
E	ILE102
E	THR104
E	TYR117
E	VAL120
E	LEU158
E	LYS208
E	THR209
E	GLY210
E	TYR211
E	ARG250
E	HOH601

site_id	AE5
Number of Residues	20
Details	binding site for Di-peptide 8FB F 501 and SER F 70

Chain	Residue
F	PRO68
F	ALA69
F	THR71
F	PHE72
F	KCX73
F	ILE102
F	THR104
F	TRP105
F	TYR117
F	VAL120
F	LEU158
F	LYS208
F	THR209
F	GLY210
F	TYR211
F	ARG250
F	HOH613
F	HOH635
F	HOH699
F	HOH728

site_id	AE6
Number of Residues	21
Details	binding site for Di-peptide 8FB G 501 and SER G 70

Chain	Residue
G	PRO68
G	ALA69
G	THR71
G	PHE72
G	KCX73
G	ILE102
G	THR104
G	TRP105
G	TYR117
G	SER118
G	VAL120
G	LEU158
G	LYS208
G	THR209
G	GLY210
G	TYR211
G	ARG250
G	HOH611
G	HOH618
G	HOH651
G	HOH663

site_id	AE7
Number of Residues	19
Details	binding site for Di-peptide 8FB H 501 and SER H 70

Chain	Residue
H	PRO68
H	ALA69
H	THR71
H	PHE72
H	KCX73
H	THR104
H	TRP105
H	TYR117
H	VAL120
H	LEU158
H	LYS208
H	THR209
H	GLY210
H	TYR211
H	LEU247
H	ARG250
H	HOH621
H	HOH631
H	HOH640

Functional Information from PROSITE/UniProt

site_id	PS00337
Number of Residues	11
Details	BETA_LACTAMASE_D Beta-lactamase class-D active site. PaSTFKIPnSL

Chain	Residue	Details
B	PRO68-LEU78
A	PRO68-LEU78

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Acyl-ester intermediate","evidences":[{"source":"PIRSR","id":"PIRSR602137-50","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"25406838","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26731698","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"31358584","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"32150407","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"4WMC","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5FAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5FAS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6P97","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6P98","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6P99","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6P9C","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"6V1O","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	24
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"Q8RLA6","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"UniProtKB","id":"P13661","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"PIRSR","id":"PIRSR602137-50","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"19477418","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"25406838","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3HBR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4WMC","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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