Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2NV1

Structure of the synthase subunit Pdx1 (YaaD) of PLP synthase from Bacillus subtilis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0006520	biological_process	amino acid metabolic process
A	0008615	biological_process	pyridoxine biosynthetic process
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	0042802	molecular_function	identical protein binding
A	0042819	biological_process	vitamin B6 biosynthetic process
A	0042823	biological_process	pyridoxal phosphate biosynthetic process
B	0005515	molecular_function	protein binding
B	0006520	biological_process	amino acid metabolic process
B	0008615	biological_process	pyridoxine biosynthetic process
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	0042802	molecular_function	identical protein binding
B	0042819	biological_process	vitamin B6 biosynthetic process
B	0042823	biological_process	pyridoxal phosphate biosynthetic process
C	0005515	molecular_function	protein binding
C	0006520	biological_process	amino acid metabolic process
C	0008615	biological_process	pyridoxine biosynthetic process
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	0042802	molecular_function	identical protein binding
C	0042819	biological_process	vitamin B6 biosynthetic process
C	0042823	biological_process	pyridoxal phosphate biosynthetic process
D	0005515	molecular_function	protein binding
D	0006520	biological_process	amino acid metabolic process
D	0008615	biological_process	pyridoxine biosynthetic process
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	0042802	molecular_function	identical protein binding
D	0042819	biological_process	vitamin B6 biosynthetic process
D	0042823	biological_process	pyridoxal phosphate biosynthetic process
E	0005515	molecular_function	protein binding
E	0006520	biological_process	amino acid metabolic process
E	0008615	biological_process	pyridoxine biosynthetic process
E	0016829	molecular_function	lyase activity
E	0016843	molecular_function	amine-lyase activity
E	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
E	0042802	molecular_function	identical protein binding
E	0042819	biological_process	vitamin B6 biosynthetic process
E	0042823	biological_process	pyridoxal phosphate biosynthetic process
F	0005515	molecular_function	protein binding
F	0006520	biological_process	amino acid metabolic process
F	0008615	biological_process	pyridoxine biosynthetic process
F	0016829	molecular_function	lyase activity
F	0016843	molecular_function	amine-lyase activity
F	0036381	molecular_function	pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity
F	0042802	molecular_function	identical protein binding
F	0042819	biological_process	vitamin B6 biosynthetic process
F	0042823	biological_process	pyridoxal phosphate biosynthetic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL A 3001

Chain	Residue
A	ARG137
A	ARG138
A	HOH4103
A	HOH4214
A	HOH4328

site_id	AC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL A 3002

Chain	Residue
A	GLY214
A	HOH4186

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 3003

Chain	Residue
A	HOH4003
A	HOH4004
F	HOH4004
F	HOH4005
A	HOH4001
A	HOH4002

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 3004

Chain	Residue
A	HOH4005
A	HOH4006
A	HOH4007
A	HOH4008
A	HOH4009
A	HOH4010

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL B 3007

Chain	Residue
B	ARG137
B	ARG138
B	HOH4100
B	HOH4327

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 3008

Chain	Residue
B	GLY153
B	GLY214
B	HOH4177

site_id	AC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 3009

Chain	Residue
A	HOH4011
A	HOH4012
A	HOH4013
B	HOH4014
B	HOH4015
B	HOH4016

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG B 3010

Chain	Residue
B	HOH4017
B	HOH4018
B	HOH4019
B	HOH4020
B	HOH4021
B	HOH4022

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL C 3013

Chain	Residue
C	ARG137
C	ARG138
C	HOH4107
C	HOH4312

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL C 3014

Chain	Residue
C	GLY214

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 3015

Chain	Residue
B	HOH4023
B	HOH4024
C	HOH4026
C	HOH4027
C	HOH4028
C	HOH4029

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 3016

Chain	Residue
C	HOH4030
C	HOH4031
C	HOH4032
C	HOH4033
C	HOH4034
C	HOH4035

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL D 3020

Chain	Residue
D	ARG137
D	ARG138
D	HOH4113
D	HOH4411

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL D 3021

Chain	Residue
D	GLY153
D	GLY214
D	HOH4128
D	HOH4171

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 3022

Chain	Residue
C	HOH4036
C	HOH4037
C	HOH4038
D	HOH4038
D	HOH4039
D	HOH4040

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 3023

Chain	Residue
D	HOH4041
D	HOH4042
D	HOH4043
D	HOH4044
D	HOH4045
D	HOH4046

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL E 3025

Chain	Residue
E	ARG137
E	ARG138
E	HOH4141

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL E 3026

Chain	Residue
E	GLY153
E	GLY214
E	HOH4190
E	HOH4428

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG D 3027

Chain	Residue
D	HOH4047
D	HOH4048
E	HOH4049
E	HOH4050
E	HOH4051
E	HOH4052

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 3028

Chain	Residue
E	HOH4053
E	HOH4054
E	HOH4055
E	HOH4056
E	HOH4057
E	HOH4058

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL F 3030

Chain	Residue
F	ARG137
F	ARG138
F	HOH4096

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL F 3031

Chain	Residue
F	HOH4254
F	GLY153
F	GLY214

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG E 3032

Chain	Residue
E	HOH4059
E	HOH4060
E	HOH4061
F	HOH4006
F	HOH4007
F	HOH4008

site_id	CC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG F 3033

Chain	Residue
F	HOH4009
F	HOH4010
F	HOH4011
F	HOH4012
F	HOH4013
F	HOH4014

site_id	CC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 3005

Chain	Residue
A	ALA186
A	LYS187
A	GLY190
A	ALA191
A	PRO192
A	PRO192
A	TYR193
A	HOH4334
A	HOH4334

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 3006

Chain	Residue
A	LYS187
A	LYS187
A	ASN188
A	GLY190
A	HOH4065
A	HOH4178
A	HOH4211

site_id	CC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 3011

Chain	Residue
B	LYS187
B	HOH4347
F	LYS187
F	ASN188
F	LEU189
F	GLY190

site_id	DC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 3012

Chain	Residue
B	LYS187
B	ALA191
B	PRO192
B	TYR193
F	GLY190
F	PRO192
F	EDO3035

site_id	DC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO C 3017

Chain	Residue
C	PRO192
C	TYR193
C	GLU194
C	LEU195
C	HOH4139
C	HOH4214
E	PRO192
E	TYR193
E	GLU194

site_id	DC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 3018

Chain	Residue
C	ALA186
C	LYS187
C	ALA191
C	PRO192
C	TYR193
E	GLY190
E	PRO192

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 3019

Chain	Residue
C	ASP24
C	LYS81
C	ASP102
C	ARG147
C	PHE233

site_id	DC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO D 3024

Chain	Residue
D	ALA186
D	LYS187
D	GLY190
D	ALA191
D	PRO192
D	PRO192
D	TYR193

site_id	DC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO E 3029

Chain	Residue
C	GLY190
C	PRO192
E	LYS187
E	ALA191
E	PRO192
E	TYR193

site_id	DC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO F 3034

Chain	Residue
B	PRO192
B	TYR193
B	GLU194
F	PRO192
F	TYR193
F	GLU194
F	LEU195
F	HOH4158

site_id	DC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO F 3035

Chain	Residue
B	GLY190
B	ALA191
B	PRO192
B	EDO3012
F	ALA186
F	LYS187
F	ALA191
F	PRO192
F	TYR193

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	LEU205-LEU223

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Schiff-base intermediate with D-ribose 5-phosphate","evidences":[{"source":"HAMAP-Rule","id":"MF_01824","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"17189272","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	30
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01824","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	1
Details	Annotated By Reference To The Literature 1g4p

Chain	Residue	Details
A	GLY128

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1g4p

Chain	Residue	Details
B	GLY128

site_id	CSA3
Number of Residues	1
Details	Annotated By Reference To The Literature 1g4p

Chain	Residue	Details
C	GLY128

site_id	CSA4
Number of Residues	1
Details	Annotated By Reference To The Literature 1g4p

Chain	Residue	Details
D	GLY128

site_id	CSA5
Number of Residues	1
Details	Annotated By Reference To The Literature 1g4p

Chain	Residue	Details
E	GLY128

site_id	CSA6
Number of Residues	1
Details	Annotated By Reference To The Literature 1g4p

Chain	Residue	Details
F	GLY128

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