Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3KUM

Crystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Arg-L-Tyr

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0006518	biological_process	peptide metabolic process
A	0009063	biological_process	amino acid catabolic process
A	0016853	molecular_function	isomerase activity
A	0016854	molecular_function	racemase and epimerase activity
A	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
A	0046872	molecular_function	metal ion binding
B	0000287	molecular_function	magnesium ion binding
B	0006518	biological_process	peptide metabolic process
B	0009063	biological_process	amino acid catabolic process
B	0016853	molecular_function	isomerase activity
B	0016854	molecular_function	racemase and epimerase activity
B	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
B	0046872	molecular_function	metal ion binding
C	0000287	molecular_function	magnesium ion binding
C	0006518	biological_process	peptide metabolic process
C	0009063	biological_process	amino acid catabolic process
C	0016853	molecular_function	isomerase activity
C	0016854	molecular_function	racemase and epimerase activity
C	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
C	0046872	molecular_function	metal ion binding
D	0000287	molecular_function	magnesium ion binding
D	0006518	biological_process	peptide metabolic process
D	0009063	biological_process	amino acid catabolic process
D	0016853	molecular_function	isomerase activity
D	0016854	molecular_function	racemase and epimerase activity
D	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
D	0046872	molecular_function	metal ion binding
E	0000287	molecular_function	magnesium ion binding
E	0006518	biological_process	peptide metabolic process
E	0009063	biological_process	amino acid catabolic process
E	0016853	molecular_function	isomerase activity
E	0016854	molecular_function	racemase and epimerase activity
E	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
E	0046872	molecular_function	metal ion binding
F	0000287	molecular_function	magnesium ion binding
F	0006518	biological_process	peptide metabolic process
F	0009063	biological_process	amino acid catabolic process
F	0016853	molecular_function	isomerase activity
F	0016854	molecular_function	racemase and epimerase activity
F	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
F	0046872	molecular_function	metal ion binding
G	0000287	molecular_function	magnesium ion binding
G	0006518	biological_process	peptide metabolic process
G	0009063	biological_process	amino acid catabolic process
G	0016853	molecular_function	isomerase activity
G	0016854	molecular_function	racemase and epimerase activity
G	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
G	0046872	molecular_function	metal ion binding
H	0000287	molecular_function	magnesium ion binding
H	0006518	biological_process	peptide metabolic process
H	0009063	biological_process	amino acid catabolic process
H	0016853	molecular_function	isomerase activity
H	0016854	molecular_function	racemase and epimerase activity
H	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
H	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ARG A 355

Chain	Residue
A	PHE19
A	THR134
A	LYS161
A	CYS292
A	ASP318
A	ASP320
A	TYR356
A	HOH771
A	HOH773

site_id	AC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE TYR A 356

Chain	Residue
A	PHE19
A	ILE21
A	PHE53
A	ILE54
A	LYS159
A	LYS161
A	ASP189
A	ASN191
A	GLU215
A	ASP240
A	LYS264
A	CYS292
A	ALA294
A	GLU295
A	ARG355
A	MG357
A	HOH385

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 357

Chain	Residue
A	ASP189
A	GLU215
A	ASP240
A	TYR356
A	HOH358

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ARG B 355

Chain	Residue
B	PHE19
B	THR134
B	LYS161
B	CYS292
B	ASP318
B	ASP320
B	TYR356
B	HOH381
B	HOH708

site_id	AC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE TYR B 356

Chain	Residue
B	ILE21
B	ILE26
B	PHE53
B	LYS159
B	LYS161
B	ASP189
B	ASN191
B	GLU215
B	ASP240
B	LYS264
B	CYS292
B	ALA294
B	GLU295
B	ARG355
B	MG357
B	HOH398

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 357

Chain	Residue
B	ASP189
B	GLU215
B	ASP240
B	TYR356
B	HOH358

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE ARG C 355

Chain	Residue
C	PHE19
C	THR134
C	LYS161
C	CYS292
C	ASP318
C	ASP320
C	TYR356
C	HOH516

site_id	AC8
Number of Residues	14
Details	BINDING SITE FOR RESIDUE TYR C 356

Chain	Residue
C	ILE21
C	PHE53
C	LYS159
C	LYS161
C	ASP189
C	ASN191
C	ASP240
C	LYS264
C	CYS292
C	ALA294
C	GLU295
C	ARG355
C	MG357
C	HOH376

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 357

Chain	Residue
C	LYS159
C	ASP189
C	GLU215
C	ASP240
C	TYR356
C	HOH358

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ARG D 355

Chain	Residue
D	PHE19
D	THR134
D	LYS161
D	CYS292
D	ASP318
D	ASP320
D	TYR356

site_id	BC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE TYR D 356

Chain	Residue
D	ILE54
D	LYS159
D	LYS161
D	ASP189
D	ASN191
D	ASP240
D	LYS264
D	CYS292
D	ALA294
D	GLU295
D	ARG355
D	MG357
D	HOH474
D	HOH562
D	ILE21
D	ILE26
D	PHE53

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 357

Chain	Residue
D	LYS159
D	ASP189
D	GLU215
D	ASP240
D	TYR356
D	HOH367

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ARG E 355

Chain	Residue
E	PHE19
E	THR134
E	LYS161
E	CYS292
E	ALA294
E	ASP318
E	ASP320
E	TYR356
E	HOH546

site_id	BC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE TYR E 356

Chain	Residue
E	ILE21
E	PHE53
E	LYS159
E	LYS161
E	ASP189
E	ASN191
E	ASP240
E	LYS264
E	CYS292
E	ALA294
E	GLU295
E	ARG355
E	MG357
E	HOH386

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 357

Chain	Residue
E	LYS159
E	ASP189
E	GLU215
E	ASP240
E	TYR356
E	HOH358

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ARG F 355

Chain	Residue
F	PHE19
F	THR134
F	LYS161
F	CYS292
F	ASP318
F	ASP320
F	TYR356

site_id	BC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE TYR F 356

Chain	Residue
F	ILE21
F	ILE26
F	PHE53
F	ILE54
F	LYS159
F	LYS161
F	ASP189
F	ASN191
F	ASP240
F	LYS264
F	CYS292
F	ALA294
F	GLU295
F	ARG355
F	MG357
F	HOH698
F	HOH784

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 357

Chain	Residue
F	LYS159
F	ASP189
F	GLU215
F	ASP240
F	TYR356
F	HOH439

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ARG G 355

Chain	Residue
G	THR134
G	LYS161
G	CYS292
G	ASP318
G	ASP320
G	TYR356

site_id	CC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE TYR G 356

Chain	Residue
G	PHE19
G	ILE21
G	ILE26
G	PHE53
G	LYS159
G	LYS161
G	ASP189
G	ASN191
G	GLU215
G	ASP240
G	LYS264
G	CYS292
G	ALA294
G	GLU295
G	ARG355
G	MG357
G	HOH372

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG G 357

Chain	Residue
G	ASP189
G	GLU215
G	ASP240
G	TYR356
G	HOH358

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE ARG H 355

Chain	Residue
H	PHE19
H	THR134
H	LYS161
H	CYS292
H	ASP318
H	ASP320
H	TYR356

site_id	CC5
Number of Residues	16
Details	BINDING SITE FOR RESIDUE TYR H 356

Chain	Residue
H	ILE21
H	ILE26
H	PHE53
H	LYS159
H	LYS161
H	ASP189
H	ASN191
H	GLU215
H	ASP240
H	LYS264
H	CYS292
H	ALA294
H	GLU295
H	ARG355
H	MG357
H	HOH412

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG H 357

Chain	Residue
H	ASP189
H	GLU215
H	ASP240
H	TYR356
H	HOH358

Functional Information from PROSITE/UniProt

site_id	PS00909
Number of Residues	32
Details	MR_MLE_2 Mandelate racemase / muconate lactonizing enzyme family signature 2. LrlDaNqawtpkdAvkaiqaLadyqielVEQP

Chain	Residue	Details
A	LEU186-PRO217

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	112
Details	Binding site: {}

Chain

Residue

Details

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