Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6GPL

Crystal structure of human GDP-D-mannose 4,6-dehydratase in complex with GDP-4k6d-Man

Functional Information from GO Data

Chain	GOid	namespace	contents
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0007219	biological_process	Notch signaling pathway
B	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
B	0016829	molecular_function	lyase activity
B	0019673	biological_process	GDP-mannose metabolic process
B	0042350	biological_process	GDP-L-fucose biosynthetic process
B	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
B	0042802	molecular_function	identical protein binding
B	0070062	cellular_component	extracellular exosome
B	0070401	molecular_function	NADP+ binding
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0007219	biological_process	Notch signaling pathway
C	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
C	0016829	molecular_function	lyase activity
C	0019673	biological_process	GDP-mannose metabolic process
C	0042350	biological_process	GDP-L-fucose biosynthetic process
C	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
C	0042802	molecular_function	identical protein binding
C	0070062	cellular_component	extracellular exosome
C	0070401	molecular_function	NADP+ binding
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0007219	biological_process	Notch signaling pathway
D	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
D	0016829	molecular_function	lyase activity
D	0019673	biological_process	GDP-mannose metabolic process
D	0042350	biological_process	GDP-L-fucose biosynthetic process
D	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
D	0042802	molecular_function	identical protein binding
D	0070062	cellular_component	extracellular exosome
D	0070401	molecular_function	NADP+ binding
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0007219	biological_process	Notch signaling pathway
E	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
E	0016829	molecular_function	lyase activity
E	0019673	biological_process	GDP-mannose metabolic process
E	0042350	biological_process	GDP-L-fucose biosynthetic process
E	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
E	0042802	molecular_function	identical protein binding
E	0070062	cellular_component	extracellular exosome
E	0070401	molecular_function	NADP+ binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	11
Details	binding site for residue BCN B 401

Chain	Residue
B	ARG64
E	SER59
E	PHE60
B	ARG213
B	ARG214
B	GLY215
B	ALA216
B	ARG221
B	LEU365
B	HOH560
B	HOH695

site_id	AC2
Number of Residues	27
Details	binding site for residue F7E B 402

Chain	Residue
B	SER112
B	HIS113
B	VAL114
B	THR155
B	SER156
B	TYR179
B	ASN208
B	ARG214
B	ASN217
B	PHE218
B	VAL219
B	LYS222
B	LEU240
B	GLY241
B	ASN242
B	ALA245
B	ARG247
B	VAL281
B	ARG325
B	GLU328
B	NAP403
B	HOH565
B	HOH575
B	HOH616
B	HOH631
B	HOH653
B	HOH663

site_id	AC3
Number of Residues	40
Details	binding site for residue NAP B 403

Chain	Residue
B	GLY30
B	THR32
B	GLY33
B	GLN34
B	ASP35
B	ARG55
B	ASN61
B	ASP86
B	LEU87
B	LEU108
B	GLY109
B	ALA110
B	SER112
B	TYR123
B	VAL127
B	ALA153
B	SER154
B	THR155
B	TYR179
B	LYS183
B	LEU206
B	ASN208
B	HIS209
B	ARG214
B	F7E402
B	EDO406
B	HOH543
B	HOH570
B	HOH575
B	HOH585
B	HOH586
B	HOH588
B	HOH590
B	HOH633
B	HOH676
B	HOH689
E	ARG56
E	SER57
E	SER58
E	HOH4225

site_id	AC4
Number of Residues	4
Details	binding site for residue EDO B 404

Chain	Residue
B	ARG176
B	PRO326
B	HOH618
C	GLU195

site_id	AC5
Number of Residues	4
Details	binding site for residue EDO B 405

Chain	Residue
B	ARG194
B	GLU195
B	EDO407
B	HOH508

site_id	AC6
Number of Residues	7
Details	binding site for residue EDO B 406

Chain	Residue
B	ARG55
B	ASN61
B	NAP403
E	ARG55
E	SER57
E	ASN61
E	NAP4002

site_id	AC7
Number of Residues	7
Details	binding site for residue EDO B 407

Chain	Residue
C	TYR174
B	TYR187
B	TRP188
B	ARG194
B	EDO405
B	HOH548
B	HOH650

site_id	AC8
Number of Residues	27
Details	binding site for residue F7E C 2001

Chain	Residue
C	SER112
C	HIS113
C	VAL114
C	THR155
C	SER156
C	TYR179
C	ASN208
C	ARG214
C	ASN217
C	PHE218
C	VAL219
C	LYS222
C	LEU240
C	GLY241
C	ASN242
C	ALA245
C	ARG247
C	VAL281
C	ARG325
C	GLU328
C	NAP2002
C	HOH2186
C	HOH2196
C	HOH2199
C	HOH2212
C	HOH2213
C	HOH2230

site_id	AC9
Number of Residues	40
Details	binding site for residue NAP C 2002

Chain	Residue
C	GLY30
C	THR32
C	GLY33
C	GLN34
C	ASP35
C	ARG55
C	ASP86
C	LEU87
C	LEU108
C	GLY109
C	ALA110
C	SER112
C	TYR123
C	VAL127
C	ALA153
C	SER154
C	THR155
C	TYR179
C	LYS183
C	LEU206
C	ASN208
C	HIS209
C	ARG214
C	F7E2001
C	HOH2135
C	HOH2164
C	HOH2171
C	HOH2175
C	HOH2212
C	HOH2217
C	HOH2226
C	HOH2233
C	HOH2236
C	HOH2249
C	HOH2257
C	HOH2268
D	ARG56
D	SER57
D	SER58
D	EDO3003

site_id	AD1
Number of Residues	7
Details	binding site for residue EDO C 2003

Chain	Residue
B	TYR174
C	TYR187
C	TRP188
C	ARG194
C	ASP270
C	HOH2110
C	HOH2146

site_id	AD2
Number of Residues	3
Details	binding site for residue EDO C 2004

Chain	Residue
C	ARG194
C	GLU195
C	HOH2107

site_id	AD3
Number of Residues	29
Details	binding site for residue F7E D 3001

Chain	Residue
D	SER112
D	HIS113
D	VAL114
D	THR155
D	SER156
D	TYR179
D	ASN208
D	ARG214
D	ASN217
D	PHE218
D	VAL219
D	LYS222
D	LEU240
D	GLY241
D	ASN242
D	ALA245
D	ARG247
D	VAL281
D	TYR323
D	ARG325
D	GLU328
D	NAP3002
D	HOH3110
D	HOH3132
D	HOH3161
D	HOH3194
D	HOH3218
D	HOH3226
D	HOH3227

site_id	AD4
Number of Residues	40
Details	binding site for residue NAP D 3002

Chain	Residue
C	ARG56
C	SER57
C	SER58
D	GLY30
D	THR32
D	GLY33
D	GLN34
D	ASP35
D	ARG55
D	ASP86
D	LEU87
D	LEU108
D	GLY109
D	ALA110
D	SER112
D	TYR123
D	VAL127
D	ALA153
D	SER154
D	THR155
D	TYR179
D	LYS183
D	LEU206
D	ASN208
D	HIS209
D	ARG214
D	F7E3001
D	EDO3003
D	HOH3114
D	HOH3120
D	HOH3132
D	HOH3164
D	HOH3186
D	HOH3189
D	HOH3191
D	HOH3198
D	HOH3200
D	HOH3204
D	HOH3219
D	HOH3232

site_id	AD5
Number of Residues	8
Details	binding site for residue EDO D 3003

Chain	Residue
C	ARG55
C	SER57
C	ASN61
C	NAP2002
D	ARG55
D	SER57
D	ASN61
D	NAP3002

site_id	AD6
Number of Residues	6
Details	binding site for residue EDO D 3004

Chain	Residue
D	TYR187
D	TRP188
D	ARG194
D	ASP270
D	HOH3169
D	HOH3197

site_id	AD7
Number of Residues	4
Details	binding site for residue EDO D 3005

Chain	Residue
D	TYR174
D	HOH3103
E	TYR187
E	TRP188

site_id	AD8
Number of Residues	29
Details	binding site for residue F7E E 4001

Chain	Residue
E	SER112
E	VAL114
E	THR155
E	SER156
E	GLU157
E	TYR179
E	ASN208
E	ARG214
E	ASN217
E	PHE218
E	VAL219
E	LYS222
E	LEU240
E	GLY241
E	ASN242
E	ALA245
E	ARG247
E	VAL281
E	TYR323
E	ARG325
E	GLU328
E	NAP4002
E	HOH4125
E	HOH4143
E	HOH4175
E	HOH4210
E	HOH4215
E	HOH4217
E	HOH4243

site_id	AD9
Number of Residues	39
Details	binding site for residue NAP E 4002

Chain	Residue
B	ARG56
B	SER57
B	SER58
B	EDO406
E	GLY30
E	THR32
E	GLY33
E	GLN34
E	ASP35
E	ARG55
E	ASP86
E	LEU87
E	LEU108
E	GLY109
E	ALA110
E	SER112
E	TYR123
E	VAL127
E	ALA153
E	SER154
E	THR155
E	TYR179
E	LYS183
E	LEU206
E	ASN208
E	HIS209
E	ARG214
E	F7E4001
E	HOH4143
E	HOH4145
E	HOH4152
E	HOH4168
E	HOH4179
E	HOH4185
E	HOH4187
E	HOH4197
E	HOH4239
E	HOH4251
E	HOH4262

Functional Information from PROSITE/UniProt

site_id	PS00061
Number of Residues	29
Details	ADH_SHORT Short-chain dehydrogenases/reductases family signature. PqkettpfypRspYGAAKLYAyWIVvNFR

Chain	Residue	Details
B	PRO166-ARG194

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Active site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	68
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2004","submissionDatabase":"PDB data bank","title":"Crystal structure and biophysical characterization of human GDP-D-mannose 4,6-dehydratase.","authors":["Vedadi M.","Walker J.R.","Sharma S.","Houston S.","Wasney G.","Loppnau P.","Oppermann U."]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

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