Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4IHC

Crystal structure of probable mannonate dehydratase Dd703_0947 (target EFI-502222) from Dickeya dadantii Ech703

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000287	molecular_function	magnesium ion binding
A	0008927	molecular_function	mannonate dehydratase activity
A	0009063	biological_process	amino acid catabolic process
A	0016052	biological_process	carbohydrate catabolic process
A	0016829	molecular_function	lyase activity
A	0046872	molecular_function	metal ion binding
A	0047929	molecular_function	gluconate dehydratase activity
B	0000287	molecular_function	magnesium ion binding
B	0008927	molecular_function	mannonate dehydratase activity
B	0009063	biological_process	amino acid catabolic process
B	0016052	biological_process	carbohydrate catabolic process
B	0016829	molecular_function	lyase activity
B	0046872	molecular_function	metal ion binding
B	0047929	molecular_function	gluconate dehydratase activity
C	0000287	molecular_function	magnesium ion binding
C	0008927	molecular_function	mannonate dehydratase activity
C	0009063	biological_process	amino acid catabolic process
C	0016052	biological_process	carbohydrate catabolic process
C	0016829	molecular_function	lyase activity
C	0046872	molecular_function	metal ion binding
C	0047929	molecular_function	gluconate dehydratase activity
D	0000287	molecular_function	magnesium ion binding
D	0008927	molecular_function	mannonate dehydratase activity
D	0009063	biological_process	amino acid catabolic process
D	0016052	biological_process	carbohydrate catabolic process
D	0016829	molecular_function	lyase activity
D	0046872	molecular_function	metal ion binding
D	0047929	molecular_function	gluconate dehydratase activity
E	0000287	molecular_function	magnesium ion binding
E	0008927	molecular_function	mannonate dehydratase activity
E	0009063	biological_process	amino acid catabolic process
E	0016052	biological_process	carbohydrate catabolic process
E	0016829	molecular_function	lyase activity
E	0046872	molecular_function	metal ion binding
E	0047929	molecular_function	gluconate dehydratase activity
F	0000287	molecular_function	magnesium ion binding
F	0008927	molecular_function	mannonate dehydratase activity
F	0009063	biological_process	amino acid catabolic process
F	0016052	biological_process	carbohydrate catabolic process
F	0016829	molecular_function	lyase activity
F	0046872	molecular_function	metal ion binding
F	0047929	molecular_function	gluconate dehydratase activity
G	0000287	molecular_function	magnesium ion binding
G	0008927	molecular_function	mannonate dehydratase activity
G	0009063	biological_process	amino acid catabolic process
G	0016052	biological_process	carbohydrate catabolic process
G	0016829	molecular_function	lyase activity
G	0046872	molecular_function	metal ion binding
G	0047929	molecular_function	gluconate dehydratase activity
H	0000287	molecular_function	magnesium ion binding
H	0008927	molecular_function	mannonate dehydratase activity
H	0009063	biological_process	amino acid catabolic process
H	0016052	biological_process	carbohydrate catabolic process
H	0016829	molecular_function	lyase activity
H	0046872	molecular_function	metal ion binding
H	0047929	molecular_function	gluconate dehydratase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 501

Chain	Residue
A	ASP223
A	GLU249
A	GLU275
A	FMT503
A	HOH698
A	HOH730

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 502

Chain	Residue
A	PRO327
A	ASP329
A	TRP404
A	HOH674
A	HOH729
B	TYR80
A	GLN43
A	HIS225
A	HIS325

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FMT A 503

Chain	Residue
A	ARG152
A	ASP223
A	GLU249
A	GLU275
A	ARG296
A	HIS325
A	GLU352
A	MG501
A	HOH660
A	HOH730

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD A 504

Chain	Residue
A	GLY116
A	LYS117
C	THR66

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 505

Chain	Residue
A	GLU27
A	THR28
A	PRO31
A	GLY32
A	LEU33
A	TYR34
A	HOH797

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD A 506

Chain	Residue
A	PRO196
A	THR229
A	THR232

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 501

Chain	Residue
B	ASP223
B	GLU249
B	GLU275
B	FMT505
B	HOH696
B	HOH744

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL B 502

Chain	Residue
A	TYR80
A	TRP81
B	GLN43
B	HIS225
B	GLU275
B	HIS325
B	PRO327
B	ASP329

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL B 503

Chain	Residue
A	HOH666
B	ARG44

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 504

Chain	Residue
A	GLU255
A	ARG416
B	ARG82
B	ASN83
B	HOH635
B	HOH698
B	HOH803

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FMT B 505

Chain	Residue
B	ASP223
B	GLU249
B	GLU275
B	ARG296
B	HIS325
B	GLU352
B	MG501
B	HOH696

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD B 506

Chain	Residue
A	ILE86
B	ILE86

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD B 507

Chain	Residue
B	THR66
D	GLY116
D	LYS117

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD B 508

Chain	Residue
B	PRO196
B	THR229
B	THR232

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG C 501

Chain	Residue
C	ASP223
C	GLU249
C	ASP250
C	GLU275
C	FMT503
C	HOH724
C	HOH783

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL C 502

Chain	Residue
C	GLN43
C	HIS225
C	GLU275
C	HIS325
C	PRO327
C	ASP329
C	HOH733
G	TYR80

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FMT C 503

Chain	Residue
C	HOH724
C	ASP223
C	GLU249
C	GLU275
C	ARG296
C	HIS325
C	GLU352
C	MG501

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL C 504

Chain	Residue
C	ARG44
G	HOH780
G	HOH826

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD C 505

Chain	Residue
C	ILE86
C	MET87
G	ILE86

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE IOD C 506

Chain	Residue
A	THR66
A	HOH752
C	GLY116
C	LYS117

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 507

Chain	Residue
C	GLU255
C	ARG416
C	HOH822
G	GLN73
G	ASN83
G	HOH743

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD C 508

Chain	Residue
C	PRO196
C	THR229
C	THR232

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 501

Chain	Residue
D	ASP223
D	GLU249
D	GLU275
D	FMT506
D	HOH724
D	HOH803

site_id	CC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 502

Chain	Residue
D	GLN43
D	HIS225
D	HIS325
D	PRO327
D	ASP329
D	FMT506
D	HOH739

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 503

Chain	Residue
D	GLU27
D	THR28
D	GLY32
D	LEU33
D	HOH823

site_id	CC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL D 504

Chain	Residue
D	ARG44

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD D 505

Chain	Residue
D	ILE86
H	GLY84
H	ILE86

site_id	DC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE FMT D 506

Chain	Residue
D	ARG152
D	ASP223
D	GLU249
D	GLU275
D	ARG296
D	HIS325
D	GLU352
D	MG501
D	GOL502
D	HOH662
D	HOH724

site_id	DC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD D 507

Chain	Residue
B	LYS117
D	THR66

site_id	DC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD D 508

Chain	Residue
D	PRO196
D	THR229
D	THR232

site_id	DC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 501

Chain	Residue
E	ASP223
E	GLU249
E	GLU275
E	FMT505
E	HOH723
E	HOH724

site_id	DC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL E 502

Chain	Residue
E	GLN43
E	HIS225
E	HIS325
E	PRO327
E	ASP329
E	TRP404
E	HOH834
F	TYR80
F	TRP81

site_id	DC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL E 503

Chain	Residue
E	ARG44
E	HOH780
F	HOH751

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL E 504

Chain	Residue
E	LYS63
E	ASP64
E	HOH606
F	HOH813

site_id	DC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FMT E 505

Chain	Residue
E	ARG152
E	ASP223
E	GLU249
E	GLU275
E	ARG296
E	HIS325
E	GLU352
E	MG501
E	HOH723
E	HOH829

site_id	DC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD E 506

Chain	Residue
E	GLY116
E	LYS117
G	THR66

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD E 507

Chain	Residue
E	THR66
G	GLY116
G	LYS117

site_id	EC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD E 508

Chain	Residue
E	PRO196
E	THR229
E	THR232

site_id	EC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 501

Chain	Residue
F	ASP223
F	GLU249
F	GLU275
F	FMT503
F	HOH682
F	HOH794

site_id	EC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL F 502

Chain	Residue
E	TYR80
E	TRP81
F	GLN43
F	HIS225
F	GLU275
F	HIS325
F	PRO327
F	ASP329
F	HOH660

site_id	EC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FMT F 503

Chain	Residue
F	ARG152
F	ASP223
F	GLU249
F	GLU275
F	ARG296
F	HIS325
F	GLU352
F	MG501
F	HOH635
F	HOH794

site_id	EC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL F 504

Chain	Residue
E	HOH737
F	ARG44

site_id	EC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD F 505

Chain	Residue
E	GLY84
E	ILE86
F	ILE86

site_id	EC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE FMT F 506

Chain	Residue
E	VAL77
F	GLU255
F	ARG416
F	HOH783
F	HOH800

site_id	EC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD F 507

Chain	Residue
F	THR66
H	GLY116
H	LYS117

site_id	FC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL F 508

Chain	Residue
F	GLU27
F	THR28
F	GLY32
F	LEU33
F	TYR34

site_id	FC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD F 509

Chain	Residue
F	PRO196
F	THR229
F	THR232

site_id	FC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG G 501

Chain	Residue
G	ASP223
G	GLU249
G	GLU275
G	FMT505
G	HOH661
G	HOH813

site_id	FC4
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GOL G 502

Chain	Residue
C	TRP81
G	GLN43
G	HIS225
G	GLU275
G	HIS325
G	PRO327
G	ASP329
G	TRP404
G	FMT505
G	HOH702
G	HOH741

site_id	FC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL G 503

Chain	Residue
G	PRO196
G	THR229

site_id	FC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL G 504

Chain	Residue
C	HOH694
G	ARG44

site_id	FC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FMT G 505

Chain	Residue
G	ASP223
G	GLU249
G	GLU275
G	ARG296
G	HIS325
G	GLU352
G	MG501
G	GOL502
G	HOH639
G	HOH813

site_id	FC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG H 501

Chain	Residue
H	ASP223
H	GLU249
H	GLU275
H	FMT505
H	HOH625
H	HOH711

site_id	FC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL H 502

Chain	Residue
D	TYR80
H	GLN43
H	HIS225
H	HIS325
H	PRO327
H	ASP329
H	HOH708

site_id	GC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL H 503

Chain	Residue
D	HOH649
H	ARG44

site_id	GC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL H 504

Chain	Residue
D	GLN73
D	ARG82
D	ASN83
H	GLU255
H	ARG416

site_id	GC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE FMT H 505

Chain	Residue
H	ARG152
H	ASP223
H	GLU249
H	GLU275
H	ARG296
H	HIS325
H	GLU352
H	MG501
H	HOH711
H	HOH800

site_id	GC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE IOD H 506

Chain	Residue
F	LYS117
H	THR66

site_id	GC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE IOD H 507

Chain	Residue
H	PRO196
H	THR229
H	THR232

Functional Information from PROSITE/UniProt

site_id	PS00908
Number of Residues	26
Details	MR_MLE_1 Mandelate racemase / muconate lactonizing enzyme family signature 1. AlSGVDmALwDIkGKlagmPVyeLLG

Chain	Residue	Details
A	ALA90-GLY115

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

Chain	Residue	Details
A	PHE220-PRO251

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	16
Details	ACT_SITE: Proton donor/acceptor => ECO:0000250

Chain	Residue	Details
A	TYR158
E	HIS225
F	TYR158
F	HIS225
G	TYR158
G	HIS225
H	TYR158
H	HIS225
A	HIS225
B	TYR158
B	HIS225
C	TYR158
C	HIS225
D	TYR158
D	HIS225
E	TYR158

site_id	SWS_FT_FI2
Number of Residues	48
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	HIS127
B	HIS325
B	ASP329
B	GLU352
C	HIS127
C	GLU275
C	ARG296
C	HIS325
C	ASP329
C	GLU352
D	HIS127
A	GLU275
D	GLU275
D	ARG296
D	HIS325
D	ASP329
D	GLU352
E	HIS127
E	GLU275
E	ARG296
E	HIS325
E	ASP329
A	ARG296
E	GLU352
F	HIS127
F	GLU275
F	ARG296
F	HIS325
F	ASP329
F	GLU352
G	HIS127
G	GLU275
G	ARG296
A	HIS325
G	HIS325
G	ASP329
G	GLU352
H	HIS127
H	GLU275
H	ARG296
H	HIS325
H	ASP329
H	GLU352
A	ASP329
A	GLU352
B	HIS127
B	GLU275
B	ARG296

site_id	SWS_FT_FI3
Number of Residues	16
Details	BINDING: BINDING => ECO:0000269\|PubMed:24697546

Chain	Residue	Details
A	ASP223
E	GLU249
F	ASP223
F	GLU249
G	ASP223
G	GLU249
H	ASP223
H	GLU249
A	GLU249
B	ASP223
B	GLU249
C	ASP223
C	GLU249
D	ASP223
D	GLU249
E	ASP223

site_id	SWS_FT_FI4
Number of Residues	8
Details	SITE: Important for activity and substrate specificity; Pro is observed in family members with low D-mannonate dehydratase activity => ECO:0000250

Chain	Residue	Details
A	PRO327
B	PRO327
C	PRO327
D	PRO327
E	PRO327
F	PRO327
G	PRO327
H	PRO327

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