Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3TNL

1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and 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

Functional Information from PDB Data

site_id	AC1
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAD A 292

Chain	Residue
A	MET74
A	ASP164
A	PHE166
A	THR210
A	GLY211
A	VAL212
A	MET214
A	PHE217
A	LEU222
A	VAL238
A	TYR240
A	ASP113
A	GLY261
A	MET264
A	MET265
A	HOH317
A	HOH471
A	HOH472
A	HOH497
A	HOH645
A	HOH860
A	HOH861
A	GLY137
A	HOH915
A	HOH952
A	HOH1208
A	HOH1511
A	HOH1702
D	HOH367
A	ALA138
A	GLY139
A	GLY140
A	ALA141
A	ASN161
A	ARG162

site_id	AC2
Number of Residues	13
Details	BINDING SITE FOR RESIDUE SKM A 293

Chain	Residue
A	LEU18
A	ILE23
A	SER26
A	SER28
A	ASN71
A	SER73
A	LYS77
A	ASN98
A	ASP113
A	GLN268
A	HOH341
A	HOH426
A	HOH1723

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL A 294

Chain	Residue
A	LYS279
A	GLU280
A	HOH984

site_id	AC4
Number of Residues	33
Details	BINDING SITE FOR RESIDUE NAD B 292

Chain	Residue
B	MET74
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	LEU222
B	VAL238
B	TYR240
B	GLY261
B	MET264
B	MET265
B	GLN268
B	HOH303
B	HOH325
B	HOH698
B	HOH1166
B	HOH1522
B	HOH1565
B	HOH1709
B	HOH1786
B	HOH1795
B	HOH1865
C	GLU274

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL B 293

Chain	Residue
B	MET74
B	PRO75
B	LYS77

site_id	AC6
Number of Residues	35
Details	BINDING SITE FOR RESIDUE NAD C 292

Chain	Residue
C	GLY211
C	VAL212
C	MET214
C	PHE217
C	VAL238
C	TYR240
C	GLY261
C	MET264
C	MET265
C	SKM293
C	HOH319
C	HOH374
C	HOH407
C	HOH433
C	HOH439
C	HOH467
C	HOH769
C	HOH1007
C	HOH1075
C	HOH1311
C	HOH1476
C	HOH1587
C	HOH1775
C	MET74
C	ASP113
C	GLY137
C	ALA138
C	GLY139
C	GLY140
C	ALA141
C	ASN161
C	ARG162
C	ASP164
C	PHE166
C	THR210

site_id	AC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE SKM C 293

Chain	Residue
C	LEU18
C	ILE23
C	SER26
C	SER28
C	ASN71
C	SER73
C	LYS77
C	ASN98
C	ASP113
C	GLN268
C	NAD292
C	HOH398
C	HOH709
C	HOH796

site_id	AC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE CL C 294

Chain	Residue
C	LYS279
C	GLU280
C	HOH885

site_id	AC9
Number of Residues	34
Details	BINDING SITE FOR RESIDUE NAD D 292

Chain	Residue
A	GLU274
D	GLY137
D	ALA138
D	GLY139
D	GLY140
D	ALA141
D	ASN161
D	ARG162
D	ASP164
D	PHE166
D	THR210
D	GLY211
D	VAL212
D	MET214
D	PHE217
D	LEU222
D	VAL238
D	TYR240
D	GLY261
D	MET265
D	GLN268
D	HOH299
D	HOH303
D	HOH324
D	HOH599
D	HOH893
D	HOH907
D	HOH929
D	HOH1045
D	HOH1141
D	HOH1273
D	HOH1486
D	HOH1767
D	HOH1817

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL D 293

Chain	Residue
D	MET74
D	PRO75
D	LYS77
D	HOH1388

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
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	8
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	36
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	16
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	4
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)