Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3FLU

Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0008652	biological_process	amino acid biosynthetic process
A	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
A	0009085	biological_process	lysine biosynthetic process
A	0009089	biological_process	lysine biosynthetic process via diaminopimelate
A	0016829	molecular_function	lyase activity
A	0019877	biological_process	diaminopimelate biosynthetic process
A	0044281	biological_process	small molecule metabolic process
B	0003824	molecular_function	catalytic activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0008652	biological_process	amino acid biosynthetic process
B	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
B	0009085	biological_process	lysine biosynthetic process
B	0009089	biological_process	lysine biosynthetic process via diaminopimelate
B	0016829	molecular_function	lyase activity
B	0019877	biological_process	diaminopimelate biosynthetic process
B	0044281	biological_process	small molecule metabolic process
C	0003824	molecular_function	catalytic activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0008652	biological_process	amino acid biosynthetic process
C	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
C	0009085	biological_process	lysine biosynthetic process
C	0009089	biological_process	lysine biosynthetic process via diaminopimelate
C	0016829	molecular_function	lyase activity
C	0019877	biological_process	diaminopimelate biosynthetic process
C	0044281	biological_process	small molecule metabolic process
D	0003824	molecular_function	catalytic activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0008652	biological_process	amino acid biosynthetic process
D	0008840	molecular_function	4-hydroxy-tetrahydrodipicolinate synthase activity
D	0009085	biological_process	lysine biosynthetic process
D	0009089	biological_process	lysine biosynthetic process via diaminopimelate
D	0016829	molecular_function	lyase activity
D	0019877	biological_process	diaminopimelate biosynthetic process
D	0044281	biological_process	small molecule metabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 292

Chain	Residue
A	ASN80
A	TYR106
A	GOL298
A	HOH309
A	HOH452
A	HOH891
B	ASN80
B	TYR106
B	GOL297

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 A 293

Chain	Residue
A	TYR133
A	ARG138
A	GLY186
A	PHE244
A	SO4294
A	HOH384

site_id	AC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 A 294

Chain	Residue
A	ALA8
A	GLY43
A	THR44
A	THR45
A	LEU101
A	TYR133
A	LYS161
A	ILE203
A	SO4293

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 295

Chain	Residue
A	LEU213
A	ARG235
A	GLN290
A	HOH378

site_id	AC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 A 296

Chain	Residue
A	HIS189
A	HOH415
A	HOH873

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 297

Chain	Residue
A	ILE19
A	HIS20
A	TYR21
A	GLU22
A	ARG25
A	HOH317

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL A 298

Chain	Residue
A	SER48
A	ALA49
A	TYR106
A	SO4292
A	HOH361
A	HOH362
A	HOH363
A	HOH509
B	ASN80
B	TYR107

site_id	AC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 299

Chain	Residue
A	TRP30
A	ASN34
A	PRO211
A	LYS212
A	HOH787
A	HOH796

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE GOL A 300

Chain	Residue
A	SER257

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL A 301

Chain	Residue
A	ASN14
A	GLN15
A	GLU263
A	HIS265
C	ASP29
C	HIS66

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 302

Chain	Residue
A	SER111
A	GLN112
A	HOH364
A	HOH368
A	HOH624

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 303

Chain	Residue
A	THR144
A	ASN145
A	ASP146
A	SER169
A	HOH772

site_id	BC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 292

Chain	Residue
B	MET1
B	GLU179
B	GLY180
B	HIS200
B	HOH398

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE SO4 B 293

Chain	Residue
B	ALA8
B	GLY43
B	THR44
B	THR45
B	LEU101
B	TYR133
B	LYS161
B	ILE203
B	SO4295

site_id	BC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE SO4 B 294

Chain	Residue
B	HIS189
B	HOH363

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 B 295

Chain	Residue
B	TYR133
B	ARG138
B	GLY186
B	PHE244
B	SO4293

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 296

Chain	Residue
A	GLU275
A	HOH645
B	TRP254
B	SER257
B	ALA258
B	PRO264

site_id	BC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL B 297

Chain	Residue
A	SO4292
B	SER48
B	ALA49
B	TYR106
B	HOH302
B	HOH304
B	HOH351
B	HOH705
A	ASN80
A	TYR107

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL B 298

Chain	Residue
B	ARG230
B	GLU231
B	ASP234
B	HOH447
D	ASN175

site_id	CC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 299

Chain	Residue
A	LYS286
A	HOH329
B	TRP30
B	ARG261
B	HOH395
B	HOH518
B	HOH570

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL B 300

Chain	Residue
B	SER111
B	GLN112
B	HOH357
B	HOH358
B	HOH614
B	HOH644

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 301

Chain	Residue
B	THR144
B	ASN145
B	ASP146
B	SER169

site_id	CC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 292

Chain	Residue
C	THR144
C	ASN145
C	SER169
C	HOH330
C	HOH352

site_id	CC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 C 293

Chain	Residue
C	ASN80
C	TYR106
C	GOL298
C	HOH315
D	ASN80
D	TYR106
D	GOL295
D	HOH369

site_id	CC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 C 294

Chain	Residue
C	ALA8
C	GLY43
C	THR44
C	THR45
C	LEU101
C	TYR133
C	LYS161
C	ILE203
C	SO4297
C	GOL303

site_id	CC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 295

Chain	Residue
C	GLY180
C	HIS200
C	HOH367

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 296

Chain	Residue
C	HIS189
C	PHE244
C	HOH397
C	HOH723

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 C 297

Chain	Residue
C	TYR133
C	ARG138
C	LYS161
C	PHE244
C	SO4294
C	HOH321

site_id	DC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 298

Chain	Residue
C	SER48
C	ALA49
C	GLY78
C	TYR106
C	SO4293
C	GOL303
C	HOH946
D	ASN80
D	TYR107

site_id	DC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL C 299

Chain	Residue
C	TRP254
C	SER257

site_id	DC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 300

Chain	Residue
B	GLU22
B	ARG25
B	HOH487
C	ASN145
C	ASP146
C	LEU149
C	GLU172

site_id	DC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 301

Chain	Residue
C	THR274
C	GLU275
C	ASN276

site_id	DC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 302

Chain	Residue
C	TRP30
C	ASN34
C	PRO211
C	LYS212
C	HOH362

site_id	DC7
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GOL C 303

Chain	Residue
C	VAL42
C	GLY43
C	THR44
C	SER48
C	GLY76
C	THR77
C	GLY78
C	LEU101
C	SER102
C	VAL103
C	SO4294
C	GOL298
C	HOH358
D	TYR107

site_id	DC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL C 304

Chain	Residue
C	LYS109
D	SO4292
D	SO4294
D	HOH379

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL C 305

Chain	Residue
C	SER111
C	GLN112
C	HOH369
C	HOH603
C	HOH765

site_id	EC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE SO4 D 292

Chain	Residue
C	GOL304
D	TYR133
D	VAL135
D	ARG138
D	ALA163
D	GLY186
D	PHE244
D	SO4293

site_id	EC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SO4 D 293

Chain	Residue
D	ALA8
D	GLY43
D	THR44
D	THR45
D	LEU101
D	TYR133
D	LYS161
D	ILE203
D	SO4292
D	GOL296

site_id	EC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 D 294

Chain	Residue
C	GOL304
D	HIS189
D	HOH322
D	HOH872

site_id	EC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL D 295

Chain	Residue
C	ASN80
C	SO4293
D	SER48
D	ALA49
D	GLY78
D	TYR106
D	GOL296
D	HOH685
D	HOH943

site_id	EC5
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GOL D 296

Chain	Residue
C	TYR107
D	VAL42
D	GLY43
D	THR44
D	SER48
D	GLY76
D	THR77
D	GLY78
D	LEU101
D	SER102
D	VAL103
D	SO4293
D	GOL295
D	HOH685

site_id	EC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 297

Chain	Residue
D	HIS20
D	TYR21
D	GLU22
D	ARG25
D	HOH629

site_id	EC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL D 298

Chain	Residue
B	HIS189
B	ASP241
B	HOH392
D	ASN166
D	GLY168
D	SER169
D	GLU172

site_id	EC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 299

Chain	Residue
A	GLN90
D	TRP254
D	SER257
D	PRO264
D	HOH648

site_id	EC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL D 300

Chain	Residue
D	ASN14
D	GLN15
D	GLU263
D	HIS265
D	HOH802

site_id	FC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL D 301

Chain	Residue
D	THR144
D	ASN145
D	ASP146
D	SER169

site_id	FC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL D 302

Chain	Residue
D	SER111
D	GLN112
D	HOH331
D	HOH364
D	HOH686
D	HOH747

Functional Information from PROSITE/UniProt

site_id	PS00665
Number of Residues	18
Details	DHDPS_1 Dihydrodipicolinate synthase signature 1. GIVavGTTGESatlsveE

Chain	Residue	Details
A	GLY38-GLU55

site_id	PS00666
Number of Residues	31
Details	DHDPS_2 Dihydrodipicolinate synthase signature 2. YNVPgrTvvsMtndtilrlaeipn.IvGVKEA

Chain	Residue	Details
A	TYR133-ALA163

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Schiff-base intermediate with substrate","evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	8
Details	Site: {"description":"Part of a proton relay during catalysis","evidences":[{"source":"HAMAP-Rule","id":"MF_00418","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
A	ARG138
A	TYR133
A	LYS161

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
B	ARG138
B	TYR133
B	LYS161

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
C	ARG138
C	TYR133
C	LYS161

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
D	ARG138
D	TYR133
D	LYS161

site_id	CSA5
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
A	THR44
A	LYS161
A	THR45

site_id	CSA6
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
B	THR44
B	LYS161
B	THR45

site_id	CSA7
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
C	THR44
C	LYS161
C	THR45

site_id	CSA8
Number of Residues	3
Details	Annotated By Reference To The Literature 1dhp

Chain	Residue	Details
D	THR44
D	LYS161
D	THR45

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