Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4ONV

Crystal structure of YagE, a KDG aldolase protein in complex with 2-Keto-3-deoxy gluconate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0016829	molecular_function	lyase activity
A	0042802	molecular_function	identical protein binding
A	0046176	biological_process	aldonic acid catabolic process
A	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
A	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0016829	molecular_function	lyase activity
B	0042802	molecular_function	identical protein binding
B	0046176	biological_process	aldonic acid catabolic process
B	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
B	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0016829	molecular_function	lyase activity
C	0042802	molecular_function	identical protein binding
C	0046176	biological_process	aldonic acid catabolic process
C	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
C	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0016829	molecular_function	lyase activity
D	0042802	molecular_function	identical protein binding
D	0046176	biological_process	aldonic acid catabolic process
D	0047440	molecular_function	2-dehydro-3-deoxy-D-pentonate aldolase activity
D	0061677	molecular_function	2-dehydro-3-deoxy-D-gluconate aldolase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 401

Chain	Residue
A	LEU54
A	PHE60
A	GLY88
A	THR89
A	GLY90
A	VAL113
A	VAL114
A	ILE115

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 402

Chain	Residue
A	PRO141
A	SER168
A	ASN169
A	THR139

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 403

Chain	Residue
A	GLU271
A	LEU275
A	LYS296
D	ARG73

site_id	AC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL A 404

Chain	Residue
A	SER123
A	GLU124

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 405

Chain	Residue
A	THR263
B	SER123
B	EDO403

site_id	AC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE KDG A 406

Chain	Residue
A	PRO20
A	PHE52
A	GLY55
A	SER56
A	GLY57
A	TYR145
A	LYS174
A	THR176
A	GLY202
A	TYR203
A	ILE219
A	SER220
A	ALA221
A	HOH532

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 401

Chain	Residue
B	PHE25
B	GLY29
B	LEU31
B	GLU67

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 402

Chain	Residue
B	LEU54
B	PHE60
B	GLY88
B	GLY90
B	VAL113
B	VAL114
B	ILE115

site_id	AC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 403

Chain	Residue
A	GOL405
B	GLU124
B	ALA125

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 404

Chain	Residue
B	ASP178
B	SER179
D	ASP178
D	SER179

site_id	BC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 405

Chain	Residue
B	GLY64
B	ALA65
B	GLU66
B	GLU67

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 406

Chain	Residue
B	THR15
B	GLY16
B	LEU211
B	ASP216
B	LEU234
B	ARG238

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 407

Chain	Residue
B	GLU66
B	LYS69
B	ALA70
B	ARG73
B	HIS103

site_id	BC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL B 408

Chain	Residue
B	GLN153
B	ASP154
B	HOH649

site_id	BC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE KDG B 409

Chain	Residue
B	PRO20
B	PHE52
B	GLY55
B	SER56
B	GLY57
B	TYR145
B	LYS174
B	THR176
B	GLY202
B	SER220
B	ALA221
B	HOH642

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO C 401

Chain	Residue
C	LEU54
C	PHE60
C	GLY88
C	THR89
C	GLY90
C	VAL113
C	ILE115
C	TYR145

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 402

Chain	Residue
C	SER123
C	GLU124
C	ALA125
C	EDO405

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 403

Chain	Residue
C	GLU124
C	ALA158
C	LEU159
C	THR162

site_id	CC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO C 404

Chain	Residue
C	SER179

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO C 405

Chain	Residue
C	SER123
C	EDO402

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 406

Chain	Residue
C	ALA164
C	ASP165
C	SER166
C	ARG167
C	SER168

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 407

Chain	Residue
B	LEU31
B	LYS33
B	PRO34
C	ASP32

site_id	CC5
Number of Residues	13
Details	BINDING SITE FOR RESIDUE KDG C 408

Chain	Residue
C	PRO20
C	PHE52
C	GLY55
C	SER56
C	GLY57
C	TYR145
C	LYS174
C	THR176
C	GLY202
C	ILE219
C	SER220
C	ALA221
C	HOH533

site_id	CC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO D 401

Chain	Residue
D	GLU66
D	LYS69

site_id	CC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 402

Chain	Residue
C	GLN62
C	PRO287
D	THR92
D	PRO117
D	TYR118
D	TYR119
D	TRP120

site_id	CC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO D 403

Chain	Residue
D	LEU54
D	PHE60
D	GLY88
D	THR89
D	GLY90
D	VAL113
D	VAL114
D	ILE115

site_id	CC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 404

Chain	Residue
D	ASP42
D	ARG278
D	HOH543

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO D 405

Chain	Residue
D	SER123
D	GLU124
D	ALA125

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 406

Chain	Residue
A	LYS33
D	ALA164
D	ASP165
D	ARG167
D	SER168

site_id	DC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL D 407

Chain	Residue
D	THR15
D	ASP216
D	ARG238

site_id	DC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 408

Chain	Residue
A	GLU293
D	LYS69
D	ARG73
D	HIS103

site_id	DC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE KDG D 409

Chain	Residue
D	PRO20
D	PHE52
D	GLY55
D	SER56
D	GLY57
D	TYR145
D	LYS174
D	THR176
D	GLY202
D	TYR203
D	ALA221
D	HOH518

Functional Information from PROSITE/UniProt

site_id	PS00665
Number of Residues	18
Details	DHDPS_1 Dihydrodipicolinate synthase signature 1. GLFflGSGGEFsqlgaeE

Chain	Residue	Details
A	GLY50-GLU67

site_id	PS00666
Number of Residues	32
Details	DHDPS_2 Dihydrodipicolinate synthase signature 2. YNFPalTgqdLtpalvktladsrsnIiGIKDT

Chain	Residue	Details
A	TYR145-THR176

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Charge relay system","evidences":[{"source":"PubMed","id":"21294156","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"source":"PubMed","id":"21294156","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Active site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"PubMed","id":"21294156","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

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