Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3TOZ

2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
A	0008652	biological_process	amino acid biosynthetic process
A	0009073	biological_process	aromatic amino acid family biosynthetic process
A	0009423	biological_process	chorismate biosynthetic process
A	0016491	molecular_function	oxidoreductase activity
A	0019632	biological_process	shikimate metabolic process
A	0050661	molecular_function	NADP binding
B	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
B	0008652	biological_process	amino acid biosynthetic process
B	0009073	biological_process	aromatic amino acid family biosynthetic process
B	0009423	biological_process	chorismate biosynthetic process
B	0016491	molecular_function	oxidoreductase activity
B	0019632	biological_process	shikimate metabolic process
B	0050661	molecular_function	NADP binding
C	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
C	0008652	biological_process	amino acid biosynthetic process
C	0009073	biological_process	aromatic amino acid family biosynthetic process
C	0009423	biological_process	chorismate biosynthetic process
C	0016491	molecular_function	oxidoreductase activity
C	0019632	biological_process	shikimate metabolic process
C	0050661	molecular_function	NADP binding
D	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
D	0008652	biological_process	amino acid biosynthetic process
D	0009073	biological_process	aromatic amino acid family biosynthetic process
D	0009423	biological_process	chorismate biosynthetic process
D	0016491	molecular_function	oxidoreductase activity
D	0019632	biological_process	shikimate metabolic process
D	0050661	molecular_function	NADP binding
E	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
E	0008652	biological_process	amino acid biosynthetic process
E	0009073	biological_process	aromatic amino acid family biosynthetic process
E	0009423	biological_process	chorismate biosynthetic process
E	0016491	molecular_function	oxidoreductase activity
E	0019632	biological_process	shikimate metabolic process
E	0050661	molecular_function	NADP binding
F	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
F	0008652	biological_process	amino acid biosynthetic process
F	0009073	biological_process	aromatic amino acid family biosynthetic process
F	0009423	biological_process	chorismate biosynthetic process
F	0016491	molecular_function	oxidoreductase activity
F	0019632	biological_process	shikimate metabolic process
F	0050661	molecular_function	NADP binding
G	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
G	0008652	biological_process	amino acid biosynthetic process
G	0009073	biological_process	aromatic amino acid family biosynthetic process
G	0009423	biological_process	chorismate biosynthetic process
G	0016491	molecular_function	oxidoreductase activity
G	0019632	biological_process	shikimate metabolic process
G	0050661	molecular_function	NADP binding
H	0004764	molecular_function	shikimate 3-dehydrogenase (NADP+) activity
H	0008652	biological_process	amino acid biosynthetic process
H	0009073	biological_process	aromatic amino acid family biosynthetic process
H	0009423	biological_process	chorismate biosynthetic process
H	0016491	molecular_function	oxidoreductase activity
H	0019632	biological_process	shikimate metabolic process
H	0050661	molecular_function	NADP binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	25
Details	BINDING SITE FOR RESIDUE NAD A 292

Chain	Residue
A	GLY137
A	THR210
A	GLY211
A	VAL212
A	MET214
A	PHE217
A	LEU222
A	VAL238
A	TYR240
A	GLY261
A	MET264
A	ALA138
A	MET265
A	GLN268
A	HOH296
A	HOH603
A	HOH705
A	HOH953
A	GLY139
A	GLY140
A	ALA141
A	ASN161
A	ARG162
A	ASP164
A	PHE166

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 293

Chain	Residue
A	MET74
A	PRO75
A	ASN76
A	LYS77
A	THR78

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 294

Chain	Residue
A	SER73
A	MET74
A	LYS77
A	ASN98
A	GLN268

site_id	AC4
Number of Residues	21
Details	BINDING SITE FOR RESIDUE NAD B 292

Chain	Residue
B	GLY137
B	ALA138
B	GLY139
B	GLY140
B	ALA141
B	ASN161
B	ARG162
B	ASP164
B	PHE166
B	THR210
B	GLY211
B	VAL212
B	MET214
B	PHE217
B	VAL238
B	TYR240
B	GLY261
B	MET264
B	MET265
B	HOH304
B	HOH329

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 293

Chain	Residue
B	SER73
B	MET74
B	LYS77
B	ASN98
B	GLN268

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 294

Chain	Residue
B	MET74
B	PRO75
B	ASN76
B	LYS77
B	THR78

site_id	AC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 295

Chain	Residue
B	PRO242
B	THR243

site_id	AC8
Number of Residues	29
Details	BINDING SITE FOR RESIDUE NAD C 292

Chain	Residue
C	ASP113
C	GLY137
C	ALA138
C	GLY139
C	GLY140
C	ALA141
C	ASN161
C	ARG162
C	ASP164
C	PHE166
C	THR210
C	GLY211
C	VAL212
C	MET214
C	PHE217
C	LEU222
C	VAL238
C	TYR240
C	GLY261
C	MET264
C	MET265
C	GLN268
C	HOH303
C	HOH305
C	HOH323
C	HOH811
C	HOH812
C	HOH965
C	HOH1009

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE CL C 293

Chain	Residue
C	HOH1019

site_id	BC1
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL C 294

Chain	Residue
C	LYS77
C	MET74

site_id	BC2
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD D 292

Chain	Residue
D	GLY137
D	ALA138
D	GLY139
D	GLY140
D	ALA141
D	ASN161
D	ARG162
D	ASP164
D	PHE166
D	THR210
D	GLY211
D	MET214
D	PHE217
D	VAL238
D	GLY261
D	MET264
D	MET265
D	GLN268
D	HOH493
D	HOH676
D	HOH819
D	HOH820

site_id	BC3
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAD E 292

Chain	Residue
E	GLY137
E	ALA138
E	GLY139
E	GLY140
E	ALA141
E	ASN161
E	ARG162
E	ASP164
E	PHE166
E	THR210
E	GLY211
E	VAL212
E	MET214
E	PHE217
E	LEU222
E	VAL238
E	TYR240
E	GLY261
E	MET264
E	MET265
E	HOH294
E	HOH393
E	HOH555
E	HOH837
E	HOH842
E	HOH1010

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE CL E 293

Chain	Residue
E	PRO231
E	GLU232

site_id	BC5
Number of Residues	25
Details	BINDING SITE FOR RESIDUE NAD F 292

Chain	Residue
F	GLY137
F	ALA138
F	GLY139
F	GLY140
F	ALA141
F	ASN161
F	ARG162
F	ASP164
F	PHE166
F	THR210
F	GLY211
F	VAL212
F	MET214
F	PHE217
F	VAL238
F	TYR240
F	GLY261
F	MET264
F	MET265
F	GLN268
F	HOH306
F	HOH615
F	HOH657
F	HOH673
F	HOH858

site_id	BC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 F 293

Chain	Residue
F	MET74
F	PRO75
F	ASN76
F	LYS77
F	THR78
F	HOH859

site_id	BC7
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAD G 292

Chain	Residue
G	GLY137
G	ALA138
G	GLY139
G	GLY140
G	ALA141
G	ASN161
G	ARG162
G	ASP164
G	THR210
G	GLY211
G	VAL212
G	MET214
G	PHE217
G	LEU222
G	VAL238
G	TYR240
G	GLY261
G	MET264
G	MET265
G	GLN268
G	HOH312
G	HOH423
G	HOH887

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 G 293

Chain	Residue
G	MET74
G	PRO75
G	ASN76
G	LYS77
G	THR78

site_id	BC9
Number of Residues	22
Details	BINDING SITE FOR RESIDUE NAD H 292

Chain	Residue
H	GLY137
H	ALA138
H	GLY139
H	GLY140
H	ALA141
H	ASN161
H	ARG162
H	ASP164
H	PHE166
H	THR210
H	GLY211
H	VAL212
H	MET214
H	PHE217
H	VAL238
H	VAL239
H	GLY261
H	MET264
H	MET265
H	HOH311
H	HOH342
H	HOH905

site_id	CC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL H 293

Chain	Residue
H	LYS131
H	LYS132
H	HOH1015

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 H 294

Chain	Residue
H	PRO242
H	THR243

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"description":"Proton acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00222","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"SEP-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of shikimate 5-dehydrogenase Listeria monocytogenes in complex with shikimate and NAD.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00222","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of shikimate 5-dehydrogenase Listeria monocytogenes in complex with shikimate and NAD.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	72
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00222","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"SEP-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of shikimate 5-dehydrogenase Listeria monocytogenes in complex with shikimate and NAD.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	32
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"SEP-2011","submissionDatabase":"PDB data bank","title":"Crystal structure of shikimate 5-dehydrogenase Listeria monocytogenes in complex with shikimate and NAD.","authoringGroup":["Center for Structural Genomics of Infectious Diseases (CSGID)"]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00222","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

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