Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4U4M

Crystal structure of 0.5M urea unfolded YagE, a KDG aldolase protein in complex with Pyruvate

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	4
Details	binding site for residue URE A 401

Chain	Residue
A	PHE147
A	THR176
A	PHE265
A	PYR404

site_id	AC2
Number of Residues	6
Details	binding site for residue URE A 402

Chain	Residue
C	ARG184
A	ASP178
A	TYR203
A	ASP205
A	PRO256
C	ALA181

site_id	AC3
Number of Residues	5
Details	binding site for residue URE A 403

Chain	Residue
A	ASN93
A	ARG95
A	GLU96
A	GLU99
B	GLU67

site_id	AC4
Number of Residues	9
Details	binding site for residue PYR A 404

Chain	Residue
A	PRO20
A	PHE52
A	GLY55
A	SER56
A	GLY57
A	TYR145
A	LYS174
A	ILE219
A	URE401

site_id	AC5
Number of Residues	6
Details	binding site for residue EDO A 407

Chain	Residue
A	LEU54
A	PHE60
A	GLY90
A	VAL113
A	ILE115
A	TYR145

site_id	AC6
Number of Residues	1
Details	binding site for residue EDO A 408

Chain	Residue
A	ALA107

site_id	AC7
Number of Residues	5
Details	binding site for residue URE B 401

Chain	Residue
B	GLY202
B	TYR203
B	ALA221
B	PHE265
B	PYR405

site_id	AC8
Number of Residues	3
Details	binding site for residue URE B 402

Chain	Residue
B	ARG73
B	ASP77
C	GLU293

site_id	AC9
Number of Residues	2
Details	binding site for residue URE B 403

Chain	Residue
B	LEU31
B	GLU67

site_id	AD1
Number of Residues	4
Details	binding site for residue URE B 404

Chain	Residue
A	ARG129
B	ASP262
B	SER289
B	PRO290

site_id	AD2
Number of Residues	7
Details	binding site for residue EDO B 406

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

site_id	AD3
Number of Residues	1
Details	binding site for residue EDO B 407

Chain	Residue
B	HIS283

site_id	AD4
Number of Residues	2
Details	binding site for residue EDO B 408

Chain	Residue
B	LYS191
B	PRO195

site_id	AD5
Number of Residues	3
Details	binding site for residue URE C 401

Chain	Residue
B	ASP77
C	GLU271
C	LYS296

site_id	AD6
Number of Residues	6
Details	binding site for residue URE D 401

Chain	Residue
D	PHE147
D	THR176
D	GLY202
D	PHE265
D	PYR403
D	HOH501

site_id	AD7
Number of Residues	4
Details	binding site for residue URE D 402

Chain	Residue
C	ARG129
D	ASP262
D	SER289
D	PRO290

site_id	AD8
Number of Residues	2
Details	binding site for residue EDO D 404

Chain	Residue
D	LYS161
D	ASP165

site_id	AD9
Number of Residues	1
Details	binding site for residue EDO D 405

Chain	Residue
D	ALA12

site_id	AE1
Number of Residues	3
Details	binding site for residue EDO D 406

Chain	Residue
D	GLY47
D	VAL48
D	ASP49

site_id	AE2
Number of Residues	14
Details	binding site for Di-peptide PYR B 405 and LYS B 174

Chain	Residue
B	PRO20
B	PHE52
B	GLY55
B	SER56
B	GLY57
B	LEU144
B	TYR145
B	ASN146
B	ILE173
B	ASP175
B	THR176
B	LEU200
B	ILE219
B	URE401

site_id	AE3
Number of Residues	13
Details	binding site for Di-peptide PYR C 402 and LYS C 174

Chain	Residue
C	LEU200
C	ILE219
C	PRO20
C	PHE52
C	GLY55
C	SER56
C	GLY57
C	LEU144
C	TYR145
C	ASN146
C	ILE173
C	ASP175
C	THR176

site_id	AE4
Number of Residues	14
Details	binding site for Di-peptide PYR D 403 and LYS D 174

Chain	Residue
D	PRO20
D	PHE52
D	GLY55
D	SER56
D	GLY57
D	LEU144
D	TYR145
D	ASN146
D	ILE173
D	ASP175
D	THR176
D	LEU200
D	ILE219
D	URE401

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	ACT_SITE: Charge relay system => ECO:0000305\|PubMed:21294156

Chain	Residue	Details
A	SER56
A	TYR119
B	SER56
B	TYR119
C	SER56
C	TYR119
D	SER56
D	TYR119

site_id	SWS_FT_FI2
Number of Residues	4
Details	ACT_SITE: Proton donor => ECO:0000305\|PubMed:21294156

Chain	Residue	Details
A	TYR145
B	TYR145
C	TYR145
D	TYR145

site_id	SWS_FT_FI3
Number of Residues	4
Details	ACT_SITE: Schiff-base intermediate with substrate => ECO:0000305\|PubMed:21294156

Chain	Residue	Details
A	LYS174
B	LYS174
C	LYS174
D	LYS174

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