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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3E8M

Structure-function Analysis of 2-Keto-3-deoxy-D-glycero-D-galacto-nononate-9-phosphate (KDN) Phosphatase Defines a New Clad Within the Type C0 HAD Subfamily

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0016787	molecular_function	hydrolase activity
A	0016788	molecular_function	hydrolase activity, acting on ester bonds
A	0046872	molecular_function	metal ion binding
B	0016787	molecular_function	hydrolase activity
B	0016788	molecular_function	hydrolase activity, acting on ester bonds
B	0046872	molecular_function	metal ion binding
C	0016787	molecular_function	hydrolase activity
C	0016788	molecular_function	hydrolase activity, acting on ester bonds
C	0046872	molecular_function	metal ion binding
D	0016787	molecular_function	hydrolase activity
D	0016788	molecular_function	hydrolase activity, acting on ester bonds
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 165

Chain	Residue
A	ASP10
A	ASP12
A	ASP103
A	HOH185
A	HOH188
A	HOH190

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL A 166

Chain	Residue
A	GLY55
A	LYS80
A	ASN106

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY A 168

Chain	Residue
A	THR34
A	SER37
A	ARG64
A	LYS67
C	MET20
C	GLU56

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE ACY A 169

Chain	Residue
A	ARG128
A	HOH405
B	ARG128
B	HOH256
B	HOH409

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEG A 170

Chain	Residue
A	HIS44
A	GLY47
A	ASP71
A	HOH272
A	HOH355

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEG A 171

Chain	Residue
A	PHE74
A	ALA83
A	GLU86
A	LEU87
A	GLU90
A	HOH443

site_id	AC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE PG4 A 172

Chain	Residue
A	ASP17
A	LYS31
A	GLY140
A	HOH184
A	HOH242
A	HOH352
B	EDO169
B	HOH201
C	HOH459
D	ASP17
D	LYS31
D	GLY140
D	HOH283
D	HOH335

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 173

Chain	Residue
A	PHE125
A	HOH267
A	HOH347
A	HOH406
B	PHE134
B	HOH222
B	HOH241
B	HOH267
B	HOH364

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 174

Chain	Residue
A	ILE160
A	ILE163
A	HOH244
A	HOH299
A	HOH303
C	LYS112
C	EDO170

site_id	BC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 175

Chain	Residue
A	ILE133
A	PHE134
A	LYS150
A	HOH224
A	HOH322
A	HOH346
D	HOH471

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 165

Chain	Residue
B	ASP10
B	ASP12
B	ASP103
B	HOH186
B	HOH188
B	HOH189

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 166

Chain	Residue
B	GLY55
B	LYS80
B	ASN106

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY B 167

Chain	Residue
A	MET20
A	GLU56
B	THR34
B	SER37
B	ARG64
B	LYS67

site_id	BC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PEG B 168

Chain	Residue
B	HIS44
B	GLY47
B	ASP71
B	HOH367
B	HOH420
B	HOH433
B	HOH434

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 169

Chain	Residue
A	PG4172
B	ASP17
B	LYS31
B	GLY140
B	HOH185
B	HOH210
B	HOH216

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 170

Chain	Residue
B	GLU66
B	LYS69
B	HOH213
A	GLU96
A	HOH261

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 171

Chain	Residue
A	LYS112
B	ILE160
B	HOH209

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 165

Chain	Residue
C	ASP10
C	ASP12
C	ASP103
C	HOH181
C	HOH183
C	HOH185

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL C 166

Chain	Residue
C	GLY55
C	LYS80
C	ASN106

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY C 167

Chain	Residue
C	THR34
C	SER37
C	ARG64
C	LYS67
D	MET20
D	GLU56

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PEG C 168

Chain	Residue
C	HIS44
C	GLY47
C	ASP71
C	HOH406

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 169

Chain	Residue
B	HOH328
C	LYS5
C	GLY47
C	ILE48
C	PRO49
C	HOH337
C	HOH393

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 170

Chain	Residue
A	ILE160
A	EDO174
C	GLU59
C	ARG62
C	HOH223
C	HOH239

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 165

Chain	Residue
D	ASP10
D	ASP12
D	ASP103
D	HOH286
D	HOH291
D	HOH294

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL D 166

Chain	Residue
D	GLY55
D	LYS80
D	ASN106

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY D 167

Chain	Residue
B	MET20
B	GLU56
D	THR34
D	SER37
D	ARG64
D	LYS67

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE ACY D 168

Chain	Residue
C	PHE125
C	ARG128
C	HOH245
C	HOH398
D	ARG128
D	HOH310

site_id	DC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE PGE D 169

Chain	Residue
C	ARG63
C	LYS67
D	TYR22
D	ASP23
D	GLY26
D	ASN27
D	GLU28
D	HOH299
D	HOH476
D	HOH497
D	HOH525

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 171

Chain	Residue
A	HOH293
D	GLU146
D	GLU149
D	LYS150
D	EDO172
D	HOH346
D	HOH372

site_id	DC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO D 172

Chain	Residue
B	PRO124
D	ARG145
D	GLU149
D	EDO171
D	HOH324
D	HOH327
D	HOH372
D	HOH412

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18986982","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23848398","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"3E84","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HGO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HGQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HGR","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18986982","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23848398","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"3E81","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3E8M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HGO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18986982","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"23848398","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"3E81","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3E84","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HGO","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"18986982","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"3E81","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3E84","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

246031

PDB entries from 2025-12-10

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