Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3RIT

Crystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg and dipeptide L-Arg-D-Lys

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 A 357

Chain	Residue
A	PRO231
C	HOH388
A	LYS232
A	HOH387
B	PRO231
B	LYS232
B	HOH395
B	HOH957
C	PRO231
C	LYS232

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 358

Chain	Residue
A	GLY246
A	PRO247
A	ALA248
A	HOH374
A	HOH540
A	HOH694
A	HOH1017

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 359

Chain	Residue
A	ARG235
A	HOH662
B	PRO257
B	HOH424
B	HOH957
C	ARG235
C	HOH390

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 360

Chain	Residue
A	ARG87
A	ARG278
A	HOH407
A	HOH1034
C	LEU123
C	ALA311
C	PRO313

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 361

Chain	Residue
A	LYS2
A	ARG77
A	ASP78
A	HOH457

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 A 362

Chain	Residue
A	THR224
A	HOH405
A	HOH1014
A	HOH1040
A	HOH1041
B	THR224
B	ARG228

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ARG A 363

Chain	Residue
A	TYR19
A	THR135
A	LYS160
A	CYS294
A	ASP296
A	ASP319
A	ASP321
A	DLY364
A	HOH403
A	HOH908

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DLY A 364

Chain	Residue
A	GLU51
A	LYS160
A	LYS162
A	ASP190
A	ASN192
A	GLU216
A	ASP241
A	GLU242
A	LYS266
A	ARG363
A	MG365

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 365

Chain	Residue
A	ASP190
A	GLU216
A	ASP241
A	GLU242
A	DLY364

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 1PE A 366

Chain	Residue
A	HIS53
A	VAL54
B	HIS53
B	VAL54
B	THR55
B	GLY56

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 357

Chain	Residue
B	GLY246
B	PRO247
B	ALA248
B	HOH364
B	HOH399
B	HOH497

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 358

Chain	Residue
B	ARG77
B	ASP78
B	HOH376

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 359

Chain	Residue
B	ARG87
B	LEU123
B	ARG278
B	ALA311
B	HOH859

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 360

Chain	Residue
A	ARG157
B	ARG157
B	HOH384

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ARG B 361

Chain	Residue
B	ASP325
B	DLY362
B	TYR19
B	THR135
B	LYS160
B	LYS162
B	CYS294
B	ASP296
B	ASP319
B	ASP321

site_id	BC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE DLY B 362

Chain	Residue
B	TYR19
B	ARG24
B	GLU51
B	LYS160
B	LYS162
B	ASP190
B	ASN192
B	GLU216
B	ASP241
B	GLU242
B	LYS266
B	MET295
B	ARG361
B	MG363

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 363

Chain	Residue
B	ASP190
B	ASN192
B	GLU216
B	ASP241
B	GLU242
B	DLY362

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 357

Chain	Residue
C	GLY246
C	PRO247
C	ALA248
C	HOH368
C	HOH614

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 358

Chain	Residue
A	LEU123
A	ALA311
A	PRO313
C	ARG87
C	ARG278
C	HOH1030

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 359

Chain	Residue
C	ARG77
C	ASP78
C	HOH400
C	HOH625

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 360

Chain	Residue
C	THR224
C	THR224
C	ARG228
C	ARG228
C	HOH1026
C	HOH1026
C	HOH1033
C	HOH1033

site_id	CC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ARG C 361

Chain	Residue
C	TYR19
C	THR135
C	LYS160
C	CYS294
C	MET295
C	ASP296
C	ASP319
C	ASP321
C	GLY322
C	DLY362

site_id	CC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE DLY C 362

Chain	Residue
C	GLU51
C	LYS160
C	LYS162
C	ASP190
C	ASN192
C	GLU216
C	ASP241
C	LYS266
C	MET295
C	ARG361
C	MG363

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG C 363

Chain	Residue
C	ASP190
C	GLU216
C	ASP241
C	GLU242
C	DLY362

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE 1PE C 364

Chain	Residue
C	VAL54
C	VAL54
C	THR55

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 357

Chain	Residue
D	GLY246
D	PRO247
D	ALA248
D	HOH382
D	HOH622

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 D 358

Chain	Residue
D	ARG87
D	ARG278
D	HOH1037
E	LEU123
E	ALA311

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 359

Chain	Residue
D	LYS2
D	ARG77
D	ASP78

site_id	DC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 D 360

Chain	Residue
D	PRO231
D	PRO231
D	PRO231
D	LYS232
D	LYS232
D	LYS232
D	HOH406
D	HOH406
D	HOH406

site_id	DC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 D 361

Chain	Residue
D	ARG235
D	ARG235
D	ARG235

site_id	DC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 362

Chain	Residue
D	THR224
D	ARG228
D	HOH1016
D	HOH1027
D	HOH1028
D	HOH1029
E	THR224
E	HOH623

site_id	DC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ARG D 363

Chain	Residue
D	TYR19
D	THR135
D	LYS162
D	CYS294
D	ASP296
D	ASP319
D	ASP321
D	ASP325
D	DLY364

site_id	DC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DLY D 364

Chain	Residue
D	ILE21
D	GLU51
D	LYS160
D	LYS162
D	ASP190
D	ASN192
D	GLU216
D	ASP241
D	ASN264
D	LYS266
D	MET295
D	ARG363
D	MG365

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 365

Chain	Residue
D	ASP190
D	ASN192
D	GLU216
D	ASP241
D	GLU242
D	DLY364

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE 1PE D 366

Chain	Residue
D	THR55
E	HIS53
E	VAL54
E	THR55
E	LEU245
E	1PE365

site_id	DC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 E 357

Chain	Residue
E	GLY246
E	PRO247
E	ALA248
E	HOH433

site_id	EC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 E 358

Chain	Residue
E	PRO231
E	PRO231
E	PRO231
E	LYS232
E	LYS232
E	LYS232

site_id	EC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 E 359

Chain	Residue
D	LEU123
D	ALA311
D	PRO313
E	ARG87
E	ARG278
E	HOH369
E	HOH1035

site_id	EC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 360

Chain	Residue
E	ARG77
E	ASP78
E	HOH378

site_id	EC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 E 361

Chain	Residue
E	ARG235
E	ARG235
E	ARG235

site_id	EC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ARG E 362

Chain	Residue
E	TYR19
E	THR135
E	LYS162
E	CYS294
E	ASP296
E	ASP319
E	ASP321
E	ASP325
E	DLY363

site_id	EC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DLY E 363

Chain	Residue
E	TYR19
E	ILE21
E	GLU51
E	LYS160
E	LYS162
E	ASP190
E	ASN192
E	GLU216
E	ASP241
E	LYS266
E	MET295
E	ARG362
E	MG364

site_id	EC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG E 364

Chain	Residue
E	ASP190
E	GLU216
E	ASP241
E	GLU242
E	DLY363

site_id	EC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE 1PE E 365

Chain	Residue
D	HIS53
D	VAL54
D	THR55
D	GLY56
D	LEU245
D	1PE366
E	GLY56

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	VAL187-PRO218

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	30
Details	Binding site: {}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	15
Details	Binding site: {"evidences":[{"source":"PubMed","id":"22392983","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	5
Details	Binding site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

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