Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4PTN

Crystal Structure of YagE, a KDG aldolase protein in complex with Magnesium cation coordinated L-glyceraldehyde

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	10
Details	BINDING SITE FOR RESIDUE EDO A 401

Chain	Residue
A	PHE52
A	TYR145
A	LEU54
A	GLY55
A	PHE60
A	GLY88
A	GLY90
A	VAL113
A	VAL114
A	ILE115

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 402

Chain	Residue
A	ASP178
A	TYR203
A	ASP205
A	HIS206
C	ALA181
C	ARG184

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GXV A 403

Chain	Residue
A	LYS174
A	THR176
A	GLY202
A	TYR203
A	ILE219
A	SER220
A	ALA221
A	PHE265
A	MG404
A	HOH524
A	HOH532

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 404

Chain	Residue
A	PRO20
A	GLY57
A	GXV403
A	HOH524
A	HOH532

site_id	AC5
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 401

Chain	Residue
B	LEU54
B	PHE60
B	GLY88
B	GLY90
B	VAL113
B	VAL114
B	ILE115
B	TYR145

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 402

Chain	Residue
B	ASP178
B	TYR203
B	ASP205
B	HIS206
B	PRO256
D	ARG184

site_id	AC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 403

Chain	Residue
B	TYR248
B	THR251
B	LEU306

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 404

Chain	Residue
B	PHE147
B	ALA149
B	ASP178
B	TYR203
B	HOH511

site_id	AC9
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL B 405

Chain	Residue
B	ASP178
D	ASP178

site_id	BC1
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GXV B 406

Chain	Residue
B	PRO20
B	LYS174
B	THR176
B	GLY202
B	TYR203
B	ILE219
B	SER220
B	ALA221
B	PHE265
B	MG407
B	HOH508
B	HOH634

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG B 407

Chain	Residue
B	PRO20
B	SER56
B	GLY57
B	GXV406
B	HOH508

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PYR B 408

Chain	Residue
A	ALA125
B	ASP262
B	SER289
B	PRO290
B	ASP292
B	HOH539
B	HOH600

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO C 401

Chain	Residue
C	LEU54
C	PHE60
C	ARG68
C	GLY88
C	THR89
C	GLY90
C	VAL113
C	VAL114
C	ILE115

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 402

Chain	Residue
A	ALA181
A	ARG184
C	ASP178
C	TYR203
C	ASP205
C	HIS206

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 403

Chain	Residue
C	HOH609
C	HOH625
C	GLY64
C	ALA65
C	GLU66
C	GLU67

site_id	BC7
Number of Residues	11
Details	BINDING SITE FOR RESIDUE GXV C 404

Chain	Residue
C	LYS174
C	THR176
C	GLY202
C	TYR203
C	ILE219
C	SER220
C	ALA221
C	PHE265
C	MG405
C	HOH528
C	HOH603

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE MG C 405

Chain	Residue
C	PRO20
C	GLY57
C	GXV404
C	HOH528

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 401

Chain	Residue
B	ALA181
B	ARG184
D	ASP178
D	TYR203
D	ASP205
D	HIS206
D	PRO256

site_id	CC1
Number of Residues	11
Details	BINDING SITE FOR RESIDUE EDO D 402

Chain	Residue
D	PHE52
D	LEU54
D	PHE60
D	ARG68
D	GLY88
D	THR89
D	GLY90
D	VAL113
D	VAL114
D	ILE115
D	TYR145

site_id	CC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GXV D 403

Chain	Residue
D	LYS174
D	GLY202
D	TYR203
D	ILE219
D	SER220
D	ALA221
D	PHE265
D	MG404
D	HOH528
D	HOH643

site_id	CC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG D 404

Chain	Residue
D	PRO20
D	SER56
D	GLY57
D	GXV403
D	HOH528

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PYR D 405

Chain	Residue
D	ASP262
D	SER289
D	PRO290
D	ASP292
D	HOH533
D	HOH586
D	HOH609

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)