Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3Q4D

Crystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0006518	biological_process	peptide metabolic 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	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	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	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	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	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	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	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
I	0000287	molecular_function	magnesium ion binding
I	0006518	biological_process	peptide metabolic process
I	0016853	molecular_function	isomerase activity
I	0016854	molecular_function	racemase and epimerase activity
I	0016855	molecular_function	racemase and epimerase activity, acting on amino acids and derivatives
I	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG A 1602

Chain	Residue
A	ASP190
A	GLU216
A	ASP241
A	ALA2473

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE DAL A 2472

Chain	Residue
A	ASP318
A	ASP320
A	THR321
A	ALA2473
A	PHE19
A	THR135
A	LYS162
A	GLY293
A	PHE294

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ALA A 2473

Chain	Residue
A	LYS160
A	LYS162
A	ASP190
A	ASN192
A	ASP241
A	LYS265
A	GLY293
A	ASP318
A	MG1602
A	DAL2472

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 1601

Chain	Residue
B	ASP190
B	ASN192
B	GLU216
B	ASP241
B	GLU242
B	ALA2471

site_id	AC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE DAL B 2470

Chain	Residue
B	PHE19
B	THR135
B	LYS162
B	GLY293
B	PHE294
B	ASP318
B	ASP320
B	THR321
B	ALA2471

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE ALA B 2471

Chain	Residue
B	LYS160
B	LYS162
B	ASP190
B	ASN192
B	GLU216
B	ASP241
B	LYS265
B	GLY293
B	ASP318
B	HOH370
B	MG1601
B	DAL2470

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 1603

Chain	Residue
C	ASP190
C	ASN192
C	GLU216
C	ASP241
C	GLU242
C	ALA2475

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE DAL C 2474

Chain	Residue
C	PHE19
C	THR135
C	LYS162
C	GLY293
C	PHE294
C	ASP318
C	ASP320
C	ALA2475

site_id	AC9
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ALA C 2475

Chain	Residue
C	LYS160
C	LYS162
C	ASP190
C	ASN192
C	GLU216
C	ASP241
C	LYS265
C	GLY293
C	ASP318
C	MG1603
C	DAL2474

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 1604

Chain	Residue
D	ASP190
D	ASN192
D	GLU216
D	ASP241
D	GLU242
D	ALA2477

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE DAL D 2476

Chain	Residue
D	PHE19
D	THR135
D	LYS162
D	GLY293
D	ASP318
D	ASP320
D	THR321
D	ALA2477

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE ALA D 2477

Chain	Residue
D	LYS160
D	LYS162
D	ASP190
D	ASP241
D	LYS265
D	GLY293
D	ASP318
D	MG1604
D	DAL2476

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 1605

Chain	Residue
E	ASN192
E	GLU216
E	ASP241
E	GLU242
E	ALA2479
E	ASP190

site_id	BC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE DAL E 2478

Chain	Residue
E	PHE19
E	THR135
E	LYS160
E	LYS162
E	GLY293
E	ASP318
E	ASP320
E	ALA2479

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ALA E 2479

Chain	Residue
E	LYS160
E	LYS162
E	ASP190
E	ASN192
E	GLU216
E	ASP241
E	LYS265
E	GLY293
E	MG1605
E	DAL2478

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 1606

Chain	Residue
F	ASP190
F	ASN192
F	GLU216
F	ASP241
F	GLU242
F	ALA2481

site_id	BC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DAL F 2480

Chain	Residue
F	THR135
F	LYS160
F	LYS162
F	GLY293
F	ASP318
F	ASP320
F	ALA2481

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ALA F 2481

Chain	Residue
F	LYS160
F	LYS162
F	ASP190
F	GLU216
F	ASP241
F	LYS265
F	GLY293
F	ASP318
F	MG1606
F	DAL2480

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG G 1607

Chain	Residue
G	ASP190
G	ASN192
G	GLU216
G	ASP241
G	GLU242
G	ALA2483

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DAL G 2482

Chain	Residue
G	PHE19
G	THR135
G	LYS162
G	GLY293
G	ASP318
G	ASP320
G	ALA2483

site_id	CC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE ALA G 2483

Chain	Residue
G	LYS160
G	LYS162
G	ASP190
G	ASN192
G	GLU216
G	ASP241
G	LYS265
G	GLY293
G	PHE294
G	MG1607
G	DAL2482

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 1608

Chain	Residue
H	ASP190
H	ASN192
H	GLU216
H	ASP241
H	GLU242
H	ALA2485

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DAL H 2484

Chain	Residue
H	PHE19
H	THR135
H	LYS162
H	GLY293
H	ASP318
H	ASP320
H	ALA2485

site_id	CC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ALA H 2485

Chain	Residue
H	LYS160
H	LYS162
H	ASP190
H	ASN192
H	GLU216
H	ASP241
H	LYS265
H	GLY293
H	MG1608
H	DAL2484

site_id	CC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG I 1609

Chain	Residue
I	ASP190
I	GLU216
I	ASP241
I	ALA2487

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE DAL I 2486

Chain	Residue
I	PHE19
I	THR135
I	LYS162
I	GLY293
I	ASP318
I	ASP320
I	ALA2487

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE ALA I 2487

Chain	Residue
I	LYS160
I	LYS162
I	ASP190
I	ASN192
I	GLU216
I	ASP241
I	LYS265
I	GLY293
I	MG1609
I	DAL2486

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	63
Details	BINDING:

Chain	Residue	Details
A	THR135
B	ASP190
B	GLU216
B	ASP241
B	LYS265
B	ASP318
C	THR135
C	LYS160
C	ASP190
C	GLU216
C	ASP241
A	LYS160
C	LYS265
C	ASP318
D	THR135
D	LYS160
D	ASP190
D	GLU216
D	ASP241
D	LYS265
D	ASP318
E	THR135
A	ASP190
E	LYS160
E	ASP190
E	GLU216
E	ASP241
E	LYS265
E	ASP318
F	THR135
F	LYS160
F	ASP190
F	GLU216
A	GLU216
F	ASP241
F	LYS265
F	ASP318
G	THR135
G	LYS160
G	ASP190
G	GLU216
G	ASP241
G	LYS265
G	ASP318
A	ASP241
H	THR135
H	LYS160
H	ASP190
H	GLU216
H	ASP241
H	LYS265
H	ASP318
I	THR135
I	LYS160
I	ASP190
A	LYS265
I	GLU216
I	ASP241
I	LYS265
I	ASP318
A	ASP318
B	THR135
B	LYS160

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