Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5K3V

apo-PDX1.3 (Arabidopsis)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0005886	cellular_component	plasma membrane
A	0006520	biological_process	amino acid metabolic process
A	0006979	biological_process	response to oxidative stress
A	0006982	biological_process	response to lipid hydroperoxide
A	0008615	biological_process	pyridoxine biosynthetic process
A	0009651	biological_process	response to salt stress
A	0010224	biological_process	response to UV-B
A	0010335	biological_process	response to non-ionic osmotic stress
A	0012505	cellular_component	endomembrane system
A	0015994	biological_process	chlorophyll metabolic process
A	0016020	cellular_component	membrane
A	0016829	molecular_function	lyase activity
A	0016843	molecular_function	amine-lyase activity
A	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
A	0042538	biological_process	hyperosmotic salinity response
A	0042803	molecular_function	protein homodimerization activity
A	0042819	biological_process	vitamin B6 biosynthetic process
A	0042823	biological_process	pyridoxal phosphate biosynthetic process
A	0046982	molecular_function	protein heterodimerization activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0005886	cellular_component	plasma membrane
B	0006520	biological_process	amino acid metabolic process
B	0006979	biological_process	response to oxidative stress
B	0006982	biological_process	response to lipid hydroperoxide
B	0008615	biological_process	pyridoxine biosynthetic process
B	0009651	biological_process	response to salt stress
B	0010224	biological_process	response to UV-B
B	0010335	biological_process	response to non-ionic osmotic stress
B	0012505	cellular_component	endomembrane system
B	0015994	biological_process	chlorophyll metabolic process
B	0016020	cellular_component	membrane
B	0016829	molecular_function	lyase activity
B	0016843	molecular_function	amine-lyase activity
B	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
B	0042538	biological_process	hyperosmotic salinity response
B	0042803	molecular_function	protein homodimerization activity
B	0042819	biological_process	vitamin B6 biosynthetic process
B	0042823	biological_process	pyridoxal phosphate biosynthetic process
B	0046982	molecular_function	protein heterodimerization activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006520	biological_process	amino acid metabolic process
C	0006979	biological_process	response to oxidative stress
C	0006982	biological_process	response to lipid hydroperoxide
C	0008615	biological_process	pyridoxine biosynthetic process
C	0009651	biological_process	response to salt stress
C	0010224	biological_process	response to UV-B
C	0010335	biological_process	response to non-ionic osmotic stress
C	0012505	cellular_component	endomembrane system
C	0015994	biological_process	chlorophyll metabolic process
C	0016020	cellular_component	membrane
C	0016829	molecular_function	lyase activity
C	0016843	molecular_function	amine-lyase activity
C	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
C	0042538	biological_process	hyperosmotic salinity response
C	0042803	molecular_function	protein homodimerization activity
C	0042819	biological_process	vitamin B6 biosynthetic process
C	0042823	biological_process	pyridoxal phosphate biosynthetic process
C	0046982	molecular_function	protein heterodimerization activity
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0005886	cellular_component	plasma membrane
D	0006520	biological_process	amino acid metabolic process
D	0006979	biological_process	response to oxidative stress
D	0006982	biological_process	response to lipid hydroperoxide
D	0008615	biological_process	pyridoxine biosynthetic process
D	0009651	biological_process	response to salt stress
D	0010224	biological_process	response to UV-B
D	0010335	biological_process	response to non-ionic osmotic stress
D	0012505	cellular_component	endomembrane system
D	0015994	biological_process	chlorophyll metabolic process
D	0016020	cellular_component	membrane
D	0016829	molecular_function	lyase activity
D	0016843	molecular_function	amine-lyase activity
D	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
D	0042538	biological_process	hyperosmotic salinity response
D	0042803	molecular_function	protein homodimerization activity
D	0042819	biological_process	vitamin B6 biosynthetic process
D	0042823	biological_process	pyridoxal phosphate biosynthetic process
D	0046982	molecular_function	protein heterodimerization activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	12
Details	binding site for residue SO4 A 401

Chain	Residue
A	PRO65
A	HOH516
A	HOH534
A	HOH549
A	GLU167
A	ALA168
A	GLY169
A	GLY229
A	GLY230
A	GLY251
A	SER252
A	HOH506

site_id	AC2
Number of Residues	9
Details	binding site for residue SO4 A 402

Chain	Residue
A	HIS131
A	GLU150
A	ARG153
A	ARG154
A	HOH557
A	HOH575
A	HOH621
B	LYS203
B	HOH529

site_id	AC3
Number of Residues	7
Details	binding site for residue EDO A 403

Chain	Residue
A	GLN31
A	ARG34
A	ARG220
A	LEU221
A	PRO222
A	VAL223
B	MET32

site_id	AC4
Number of Residues	2
Details	binding site for residue CL A 404

Chain	Residue
A	ASN295
C	LEU125

site_id	AC5
Number of Residues	1
Details	binding site for residue CL A 405

Chain	Residue
C	ASN295

site_id	AC6
Number of Residues	10
Details	binding site for residue SO4 B 401

Chain	Residue
B	ALA168
B	GLY169
B	GLY229
B	GLY230
B	GLY251
B	SER252
B	HOH503
B	HOH528
B	HOH535
B	HOH552

site_id	AC7
Number of Residues	7
Details	binding site for residue SO4 B 402

Chain	Residue
A	LYS203
A	HOH599
B	HIS131
B	GLU150
B	ARG153
B	ARG154
B	HOH603

site_id	AC8
Number of Residues	6
Details	binding site for residue EDO B 403

Chain	Residue
B	GLN31
B	ARG220
B	LEU221
B	PRO222
B	VAL223
B	VAL224

site_id	AC9
Number of Residues	11
Details	binding site for residue SO4 C 401

Chain	Residue
C	PRO65
C	GLU167
C	GLY169
C	GLY229
C	GLY230
C	GLY251
C	SER252
C	HOH503
C	HOH512
C	HOH543
C	HOH552

site_id	AD1
Number of Residues	7
Details	binding site for residue SO4 C 402

Chain	Residue
C	HIS131
C	GLU150
C	ARG153
C	ARG154
C	HOH501
C	HOH594
D	LYS203

site_id	AD2
Number of Residues	7
Details	binding site for residue EDO C 403

Chain	Residue
C	GLN31
C	ARG34
C	ARG220
C	LEU221
C	PRO222
C	VAL223
C	VAL224

site_id	AD3
Number of Residues	10
Details	binding site for residue SO4 D 401

Chain	Residue
D	PRO65
D	GLU167
D	ALA168
D	GLY169
D	GLY229
D	GLY230
D	GLY251
D	SER252
D	HOH522
D	HOH531

site_id	AD4
Number of Residues	7
Details	binding site for residue SO4 D 402

Chain	Residue
C	LYS203
C	HOH572
D	HIS131
D	GLU150
D	ARG153
D	ARG154
D	HOH507

site_id	AD5
Number of Residues	6
Details	binding site for residue CL D 403

Chain	Residue
D	PRO208
D	TYR209
D	HOH584
C	PRO208
C	TYR209
C	HOH575

site_id	AD6
Number of Residues	1
Details	binding site for residue CL D 404

Chain	Residue
D	ASN295

site_id	AD7
Number of Residues	2
Details	binding site for residue CL D 405

Chain	Residue
B	ASN295
D	LEU125

Functional Information from PROSITE/UniProt

site_id	PS01235
Number of Residues	19
Details	PDXS_SNZ_1 PdxS/SNZ family signature. LPVVQFAAGGVATPADAAL

Chain	Residue	Details
A	LEU221-LEU239

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Schiff-base intermediate with D-ribose 5-phosphate => ECO:0000250\|UniProtKB:O59080

Chain	Residue	Details
A	LYS97
B	LYS97
C	LYS97
D	LYS97

site_id	SWS_FT_FI2
Number of Residues	16
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:O59080

Chain	Residue	Details
A	ASP40
C	GLY169
C	GLY230
C	GLY251
D	ASP40
D	GLY169
D	GLY230
D	GLY251
A	GLY169
A	GLY230
A	GLY251
B	ASP40
B	GLY169
B	GLY230
B	GLY251
C	ASP40

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000250\|UniProtKB:Q03148

Chain	Residue	Details
A	ARG181
B	ARG181
C	ARG181
D	ARG181

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N-acetylmethionine => ECO:0007744\|PubMed:22223895

Chain	Residue	Details
A	MET1
B	MET1
C	MET1
D	MET1

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